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  • Bioconductor 3.19 Released

May 1, 2024

Bioconductor:

We are pleased to announce Bioconductor 3.19, consisting of 2300 software packages, 430 experiment data packages, 926 annotation packages, 30 workflows and 5 books.

There are 80 new software packages, 10 new data experiment packages, 5 new annotation packages, no new workflows, 1 new book, and many updates and improvements to existing packages.

Bioconductor 3.19 is compatible with R 4.4, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher, macOS arm64 and Linux arm64. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

Getting Started with Bioconductor 3.19

To update to or install Bioconductor 3.19

  1. Install R 4.4. Bioconductor 3.19 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 80 new software packages in this release of Bioconductor.

  • AlphaMissenseR The AlphaMissense publication https://www.science.org/doi/epdf/10.1126/science.adg7492 outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo https://zenodo.org/record/10813168 include, for instance, 71M variants across hg19 and hg38 genome builds. The ‘AlphaMissense’ package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into R and Bioconductor workflows.

  • Banksy Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell’s own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

  • BERT Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

  • betaHMM A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.

  • bettr bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.

  • biocroxytest This package provides a roclet for roxygen2 that identifies and processes code blocks in your documentation marked with @longtests. These blocks should contain tests that take a long time to run and thus cannot be included in the regular test suite of the package. When you run roxygen2::roxygenise with the longtests_roclet, it will extract these long tests from your documentation and save them in a separate directory. This allows you to run these long tests separately from the rest of your tests, for example, on a continuous integration server that is set up to run long tests.

  • BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.

  • CaMutQC CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.

  • ClustAll Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types).

  • ClusterFoldSimilarity This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

  • CRISPRball A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

  • crisprShiny Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

  • CTexploreR The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes’ main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

  • cypress CYPRESS is a cell-type-specific power tool. This package aims to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix). It can solve the cell-type mixture proportions from the reference free panel from TOAST and conduct tests to identify cell-type-specific differential expression (csDE) genes.

  • CytoMDS This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the ‘distances’ between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover’s Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

  • Damsel Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.

  • dar Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.

  • DegCre DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

  • DeProViR Emerging infectious diseases, exemplified by the zoonotic COVID-19 pandemic caused by SARS-CoV-2, are grave global threats. Understanding protein-protein interactions (PPIs) between host and viral proteins is essential for therapeutic targets and insights into pathogen replication and immune evasion. While experimental methods like yeast two-hybrid screening and mass spectrometry provide valuable insights, they are hindered by experimental noise and costs, yielding incomplete interaction maps. Computational models, notably DeProViR, predict PPIs from amino acid sequences, incorporating semantic information with GloVe embeddings. DeProViR employs a Siamese neural network, integrating convolutional and Bi-LSTM networks to enhance accuracy. It overcomes the limitations of feature engineering, offering an efficient means to predict host-virus interactions, which holds promise for antiviral therapies and advancing our understanding of infectious diseases.

  • dinoR dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR’s quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category.

  • epiregulon Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

  • epiregulon.extra Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

  • faers The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

  • findIPs Feature rankings can be distorted by a single case in the context of high-dimensional data. The cases exerts abnormal influence on feature rankings are called influential points (IPs). The package aims at detecting IPs based on case deletion and quantifies their effects by measuring the rank changes (DOI:10.48550/arXiv.2303.10516). The package applies a novel rank comparing measure using the adaptive weights that stress the top-ranked important features and adjust the weights to ranking properties.

  • GeDi The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

  • ggtreeSpace This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.

  • ginmappeR Provides functionalities to translate gene or protein identifiers between state-of-art biological databases: CARD (https://card.mcmaster.ca/), NCBI Protein, Nucleotide and Gene (https://www.ncbi.nlm.nih.gov/), UniProt (https://www.uniprot.org/) and KEGG (https://www.kegg.jp). Also offers complementary functionality like NCBI identical proteins or UniProt similar genes clusters retrieval.

  • gINTomics gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.

  • GrafGen To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

  • gypsum Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

  • hdxmsqc The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

  • HicAggR This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.

  • HybridExpress HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

  • igvShiny This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

  • iSEEfier iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).

  • knowYourCG knowYourCG automates the functional analysis of DNA methylation data. The package tests the enrichment of discrete CpG probes across thousands of curated biological and technical features. GSEA-like analysis can be performed on continuous methylation data query sets. knowYourCG can also take beta matrices as input to perform feature aggregation over the curated database sets.

  • limpca This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

  • lute Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.

  • MAPFX MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend’s LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

  • methodical DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

  • methyLImp2 This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

  • MGnifyR Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

  • MIRit MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

  • mobileRNA Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.

  • mosdef This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

  • motifTestR Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.

  • multistateQTL A collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package ‘multistateQTL’ contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a ‘QTLExperiment’ object, which is based on the ‘SummarisedExperiment’ framework.

  • pathlinkR pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

  • Pedixplorer Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

  • pgxRpi The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

  • PIPETS PIPETS provides statistically robust analysis for 3’-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks.

  • PIUMA The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

  • PLSDAbatch A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.

  • pwalign The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

  • rawDiag Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.

  • rBLAST Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

  • saseR saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: BamtoAspliCounts, convertASpli, calculateOffsets, saseRfindEncodingDim, saseRfitFor. information upon how to use these functions, check out our vignette and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. https://doi.org/10.1101/2023.06.29.547014.

  • scMitoMut This package is designed for analyzing mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation filtering and visualization. In the future, the visualization tool will become an independent package. Mutation filtering is performed by fitting a statistical model to account for various sources of noise, including PCR error, sequencing error, mtDNA sampling and/or heteroplasmy dynamics. The model tests whether the observed allele frequency of a locus in a cell can be explained by the noise model. If not, we classify it as a mutation. The input for this analysis is the allele frequency. The noise model consists of three independent models: binomial, binomial-mixture, and beta-binomial models.

  • scMultiSim scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.

  • shiny.gosling A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps.

  • simPIC simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.

  • SingleCellAlleleExperiment Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

  • sketchR Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.

  • smartid This package enables automated selection of group specific signature, especially for rare population. The package is developed for generating specifc lists of signature genes based on Term Frequency-Inverse Document Frequency (TF-IDF) modified methods. It can also be used as a new gene-set scoring method or data transformation method. Multiple visualization functions are implemented in this package.

  • smoothclust Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.

  • SpaceMarkers Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.

  • spillR Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

  • spoon This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.

  • SpotSweeper Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with ‘SpatialExperiment’ objects.

  • SurfR Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.

  • tidyCoverage tidyCoverage framework enables tidy manipulation of collections of genomic tracks and features using tidySummarizedExperiment methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on CoverageExperiment and AggregatedCoverage classes. This accelerates the integration of genomic track data in genomic analysis workflows.

  • tidyomics The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

  • tidySpatialExperiment tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.

  • tpSVG The goal of tpSVG is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, tpSVG introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the tpSVG models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.

  • transmogR transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

  • treeclimbR The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

  • txdbmaker A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

  • UCSC.utils A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

  • UPDhmm Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).

  • VisiumIO The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

New Data Experiment Packages

There are 10 new data experiment packages in this release of Bioconductor.

  • curatedPCaData The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in.

  • CytoMethIC This package provides DNA methylation-based prediction of cancer type, molecular signature and clinical outcomes. It provides convenience functions for missing value imputation, probe ID conversion, model interpretation and visualization. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC and EPICv2.

  • homosapienDEE2CellScore This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore.

  • JohnsonKinaseData The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine kinases originally published in Johnson et al. 2023. It includes gene annotation for each kinase PWM and PWM matching scores for a set of 85603 curated human phosphosites which can be used to map a PWM score to its percentile rank. The package also includes basic functionality to score user provided phosphosites.

  • MouseAgingData The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata.

  • muleaData ExperimentHubData package for the ‘mulea’ comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers. Please see the NEWS file for a list of changes in each version.

  • scaeData Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment. The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics. Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files. The resulting output from scIGD constitutes to the contents of this data package.

  • SubcellularSpatialData This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled “Library size confounds biology in spatial transcriptomics data”. Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented.

  • TENxXeniumData Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image.

  • TransOmicsData Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human.

New Annotation Packages

There are 5 new annotation packages.

  • ath1121501frmavecs Annotation package for the implementation of the frozen Robust Multiarray Analysis procedure for Arabidopsis thaliana. This package was generated on the basis of frmaTools version 1.52.0.

  • EPICv2manifest A data.frame containing an extended probe manifest for the Illumina Infinium Methylation v2.0 Kit. Contains the complete manifest from the Illumina-provided EPIC-8v2-0_EA.csv, plus additional probewise information described in Peters et al. (2024).

  • IlluminaHumanMethylationEPICv2anno.20a1.hg38 An annotation package for Illumina’s EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

  • IlluminaHumanMethylationEPICv2manifest A manifest package for Illumina’s EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

  • MafH5.gnomAD.v4.0.GRCh38 Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 4.0) for the human genome version GRCh38.

New Workflow Packages

There are no new workflow packages in this release of Bioconductor.

New Online Books

There is one new online book.

  • OHCA The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.

NEWS from existing Software Packages

a4

                   Changes in version 1.51.1
  • add Suggests: hgu95av2.db

ADaCGH2

             Changes in version 2.43.1 (2024-02-06)
  • Removed dependency from snapCGH (and functionality related to snapCGH). The snapCGH package was deprecated in Bioconductor 3.18 and removed in 3.19.

adverSCarial

             Changes in version 1.1.2 (2024-02-04)
  • Add the “decile+x” modifications

affxparser

             Changes in version 1.75.2 (2024-02-06)

Bug Fixes

  • Fixed one sprintf-related coercion issue, reported by the GCC compiler, that would produce an incorrect warning message.

  • Fixed two sprintf-related flag issues, reported by the GCC compiler, in internal assertions, which would never be reached.

               Changes in version 1.75.1 (2024-02-05)

Documentation

  • Fix incorrectly documented arguments in a few functions.

               Changes in version 1.75.0 (2023-10-24)

Notes

  • The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.19 for R (>= 4.4.0).

AHMassBank

                     Changes in version 1.3

AHMassBank 1.3.1

  • Add MassBank releases 2023.06, 2023.09 and 2023.11.

alevinQC

                   Changes in version 1.19.3

  • Minor fixes to adapt to changes in ggplot2

                     Changes in version 1.19.2

  • Add ‘Close app’ button to close the shiny application and return data

AlphaMissenseR

                    Changes in version 1.0.0
  • (v. 0.99.21) Update Zenodo data source to record 10813168, with more accessible ‘CC-BY-4.0’ license.
  • (v. 0.99.16) Housekeeping
  • Order vignettes introduction, visualization, issues.
  • Use rjsoncons (>= 1.0.1), so that jsonlite is not a hard dependency.
  • Acknowledge additional funding sources; add ImmunoOncology biocViews term.
  • (v. 0.99.15) Respond to Bioconductor reviewer comments
  • Use BiocBaseUtils for input assertions.
  • Include range join SQL directly rather than via a non-exported function.
  • Report file size when downloading.
  • Improve test coverage.
  • See GitHub issue comment; thanks @LiNk-NY
  • (v. 0.99.11) Use an S4 class for alphamissense_connection, extending duckdb_connection.
  • (v. 0.99.10) Introduce visualization on AlphaFold predictions.
  • (v. 0.99.9) Update maintainer email address, add ‘Resource unavailable’ section to ‘Issues & Solutions’ vignette.
  • (v. 0.99.7) Update to revised Zenodo API.
  • (v. 0.99.5) BREAKING change. Requires duckdb >= 0.9.1, which cannot read DuckDB databases created with earlier versions. Also introduces changes to local cache naming. See the ‘Issues & Solutions’ vignette.
  • (v. 0.99.4) Change back to Bioconductor ‘Software’ package, to allow for regular testing of data access code.
  • (v. 0.99.1) Change to Bioconductor ‘Annotation’ package.

  • (v. 0.99.1) Update to change in Zenodo API.

                     Changes in version 0.99.0
  • (v. 0.0.18) Rename (including updating existing tables) ‘#CHROM’ to ‘CHROM’ in hg19 / hg38 tables
  • (v. 0.0.17) Initial Bioconductor submission.

AnnotationHub

                   Changes in version 3.11.0

BUG CORRECTION

  • (3.11.4) Correct subsetting. Didn’t account for multiple files associated with single entry (ie. bam/bai).

AnVIL

                   Changes in version 1.16.0

USER VISIBLE CHANGES

  • (v 1.15.10) Validate API versions against hardcoded variables; produce warning when discordant (@LiNk-NY, #101).

  • (v 1.15.8) Add gcloud_storage() and gcloud_storage_buckets() to create and manage Google Cloud Storage buckets (@LiNk-NY, #72).

  • Gen3 services, avworkflow*_configuration() functions, install(), repository(), and repositories() are defunct.

  • (v 1.15.5) Catch avtable_import_status() errors in the response object.

  • (v 1.15.1) Update vignette with examples for avworkflow_info() (@mtmorgan, @yubocheng).

BUG FIXES AND MINOR IMPROVEMENTS

  • (v 1.15.11) Update Dockstore API file, version, and URL

  • (v 1.15.9) Use assertions from BiocBaseUtils

  • (v 1.15.7) Use URLencode for table in avtable and direct request to Rawls endpoint (@LiNk-NY, #98)

  • (v 1.15.6) Update the Dockstore API reference URL and use api_referenc_url instead of API file (@LiNk-NY).

  • Update namespace in vignette and examples (@kozo2, #54)

AnVILWorkflow

                    Changes in version 1.2.6

  • New function getWorkflowConfig is added and the output from this function is now required as an input for the config argument of currentInput, udpateInput, and runWorkflow functions. This change makes the execution of different functions faster because they don’t need to access AnVIL everytime to get the configuration.

  • New function AnVILBrowse is added

ATACseqQC

                   Changes in version 1.27.4

  • Fix the refresh issue for IGVSnapshot.R

                     Changes in version 1.27.3

  • Fix the issue if no single end reads in the PE bam files for shiftGAlignmentsList.R

                     Changes in version 1.27.2

  • Try to decrease the memory cost for shiftGAlignmentsList.R

                     Changes in version 1.27.1

  • Fix the issue caused by readGAlignmentsList does not support read by chunk

ATACseqTFEA

                    Changes in version 1.5.1
  • add function importFimoBindingSites.

atena

             Changes in version 1.10.0 (2024-04-27)

USER VISIBLE CHANGES

  • Annotation metadata is now propagated to parameter and resulting SummarizedExperiment objects, which can be retrieved using ‘mcols(features(x))’ and ‘mcols(rowRanges(x))’ methods, respectively.

  • The TE subclass annotation getter functions ‘getLTRs()’, ‘getLINEs()’, ‘getSINEs()’ and ‘getDNAtransposons()’ work now with both, parameter and resulting SummarizedExperiment objects.

  • Manual pages and the vignette have been updated to illustrate the previous changes.

BUG FIXES

  • Several bug fixes, mostly in how annotation metadata was stored and propagated.

AUCell

                    Changes in version 1.25
  • Remove shiny app to modify thresholds as rbokeh is deprecated.

bacon

                   Changes in version 1.32.0

NEW FEATURES

  • Added Random number generator arguments to bacon-function, globalSeed and parallelSeed that are passed to BiocParallel such that proper confidence intervals can be calculated for the estimated variables (see the example in the vignette). Thanks to Kendra Ferrier who made this contribution.

BANDITS

                   Changes in version 1.18.1
  • Updated from C++11 to C++17

Banksy

                   Changes in version 0.99.8

  • Add feature scaling options for PCA and UMAP

                     Changes in version 0.99.7

  • SCE/SPE-compatible

BASiCS

             Changes in version 2.15.4 (2024-03-25)

  • Minor bug fixe in the subset method for BASiCS_Chain objects

               Changes in version 2.15.2 (2023-12-22)

  • Minor bug fixes

BatchQC

                   Changes in version 1.99.00

Changes made to dendrogram

  • Added dendrogram_color_palette.R for coloring dendrogram
  • Updated dendrogram.R allowing batch & category to plot together

benchdamic

             Changes in version 1.9.4 (2024-03-07)

  • Re-added corncob (due to its previous removal from CRAN)

  • Bug-fix: correct DA_Seurat() due to changes of Seurat::FindMarkers()

  • Computed DA direction for ANCOM method

               Changes in version 1.9.1 (2023-11-04)

  • Temporarily removed corncob (due to its removal from CRAN)

               Changes in version 1.9.0 (2023-10-24)

  • Bump x.y.z version to odd y following creation of RELEASE_3_18 branch

               Changes in version 1.8.1 (2023-11-04)

  • Porting the changes of devel version 1.9.1 to release

BERT

                   Changes in version 0.99.0

  • BERT has been released.

  • BERT provides an hierarchical approach to batch effect adjustment with tolerance to missing values. BERT has been found to outperform similar algorithmms, e.g. HarmonizR with regard to execution time, preservation of numerical values in the input data and flexibility wrt. covariables and references.

  • The authors can be contacted via the BioConductor forum, GitHub issues and via email.

betaHMM

                   Changes in version 0.99.0

betaHMM VERSION 0.1.x - 0.99.0

  • Initial development version of betaHMM.

bettr

                   Changes in version 0.99.3

  • Add button to close app and return data

                     Changes in version 0.99.2
  • Update installation instructions

  • Expand vignette

                     Changes in version 0.99.1

  • Add R (>= 4.4.0) to Depends

                     Changes in version 0.99.0
  • Ready for submission to Bioconductor
  • Add assembleSE() function to create a summary SE

bioCancer

                   Changes in version 1.30.07

  • fix issues in Networking Tab

                     Changes in version 1.30.06

  • Merge mutation and Genetic Ptofile tabs

                     Changes in version 1.30.05

  • rewrite the function getListProfData

  • Omit function getMegaProfData user for genlist upper that 500.

                     Changes in version 1.30.04

  • update ReactomeFI2021.RDS

  • update DisGeNet0223.RDS

                     Changes in version 1.30.03

  • update documentatio with new webapi

  • progress in migration

                     Changes in version 1.30.02

  • Start migration of cBioportal tab with the new cBioPortal webAPI

                     Changes in version 1.30.01

  • Update api link

BiocBaseUtils

                    Changes in version 1.6.0

New features

  • checkInstalled allows to check if a package is installed and produces copy-and-paste text for installation.

BiocCheck

                   Changes in version 1.40.0

NEW FEATURES

  • Check for duplicate chunk labels in vignettes and produce an error when present (@hpages, #199)

  • Warn when Rnw vignettes are present (@jwokaty, #190)

  • Add error when maintainer email not parse-able in DESCRIPTION

  • Check for Bioconductor dependencies in the Imports and Depends fields; if none, produce a warning (@vjcitn).

  • Remove redundant DESCRIPTION and NAMESPACE consistency checks; these are already included in R CMD check

BUG FIXES AND MINOR IMPROVEMENTS

  • Produce NOTE instead of WARNING for infrastructure packages without Bioconductor dependencies

  • % \VignetteEngine tags with spaces were not recognized; this has been fixed

  • Skip \value checks for package and class documentation; \formats checked for data documentation

  • Delegate system calls to devtools::build to build packages

  • Update checkRbuildignore to flag test and longtests entries appropriately (@hpages, #197)

  • Fix issue where BiocCheck would fail when errors caused by duplicate chunk labels were present (@hpages, #199)

  • Avoid format checks e.g., length, indentation, and tabs for Rd files that use roxygen2

  • Use the tools:::analyze_licenses function to check for restrictive license use (@hpages, #119)

  • Use httr2 over httr for http requests

  • Clarify NOTE and WARNING messages for CITATION file inclusion (#209).

BiocFileCache

                    Changes in version 2.11

BUG FIX

  • (2.11.1) Merge PR to fix dbplyr compatibility issue

BiocHubsShiny

                    Changes in version 1.4.0
  • No significant changes.

BiocIO

                   Changes in version 1.14.0
  • No significant changes.

BioCor

                    Changes in version 1.28
  • Update tests to latest testthat change.

BiocPkgTools

                   Changes in version 1.22.0

SIGNIFICANT USER-VISIBLE CHANGES

  • biocLastBuildDate has been removed from the package.

  • Added a recursive = FALSE argument to pkgBiocDeps.

  • Add biocBuildStatusDB function to download and parse build status info from BBS artifact.

  • Include hasBiocMaint to check if a package is maintained by a particular email address (default to Bioconductor maintainer email).

BUG FIXES AND MINOR IMPROVEMENTS

  • Use all pkgType options in pkgBiocDeps and pkgBiocRevDeps.

  • Add example to buildPkgDependencyGraph using packages from biocMaintained.

  • Include an example using networkD3 in buildPkgDependencyGraph.

biocroxytest

                   Changes in version 0.99.2

Bug fixes

  • Remove .Rproj file

                     Changes in version 0.99.1

Bug fixes

  • Add files to .gitignore

                     Changes in version 0.99.0

New features

  • Initial Bioconductor submission

biomaRt

                   Changes in version 2.60.0

USER VISIBLE CHANGES

  • listEnsemblGenomes() and useEnsemblGenomes() now have a host argument, allowing you to select an Ensembl Genomes archive site. (Thanks to Hervé Pagès @hpages for the suggestion: https://github.com/grimbough/biomaRt/issues/93)

INTERNAL CHANGES

  • Removed dependency on XML package and switched all functionality to xml2

  • Swiched from httr to httr2 package for submitting queries to BioMart servers.

Biostrings

                   Changes in version 2.72.0

NEW FEATURES

  • Increase size of IO buffer from 20001 to 200000 in read_fasta_files.c and read_fastq_files.c. With this change readDNAStringSet() and family support FASTA/FASTQ files with lines up to 200000 characters. See https://github.com/Bioconductor/Biostrings/issues/59

  • Add get_XStringSet_width() to Biostrings C interface.

SIGNIFICANT USER-VISIBLE CHANGES

  • pairwiseAlignment() and related have moved to the new pwalign package. List of functions that are now implemented in pwalign:
    • pairwiseAlignment
    • PairwiseAlignments
    • PairwiseAlignmentsSingleSubject
    • writePairwiseAlignments
    • alignedPattern
    • alignedSubject
    • insertion
    • deletion
    • unaligned
    • aligned
    • indel
    • nindel
    • nedit
    • pid
    • mismatchTable
    • mismatchSummary
    • compareStrings
    • stringDist
    • nucleotideSubstitutionMatrix
    • errorSubstitutionMatrices
    • qualitySubstitutionMatrices Note that they are still temporarily defined in Biostrings but now they just call the corresponding function in pwalign. Since this is a temporary redirect, the user also gets a warning that tells them to use the fully qualified name (e.g. pwalign::pairwiseAlignment()) to call the function.
  • The BLOSUM and PAM scoring matrices have also moved to the new pwalign package. List of scoring matrices that are now located in pwalign: BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM100, PAM30, PAM40, PAM70, PAM120, PAM250.

DEPRECATED AND DEFUNCT

  • Deprecate matchprobes() and longestConsecutive().

  • needwunsQS() is now defunct (after being deprecated for 15+ years).

BUG FIXES

  • Detect buffer overflow in writeXStringSet() and raise error instead of crash. See https://github.com/Bioconductor/Biostrings/issues/20

  • Make sure read*StringSet() closes all input file handles when done. See https://support.bioconductor.org/p/9157031/

bnbc

                    Changes in version 1.25

  • Fixed an issue with build error because of missing Suggests

  • Added support for cooler files using HiCBricks (this happened in an earlier verion).

  • Various documentation fixes.

BREW3R.r

                   Changes in version 0.99.2

  • Fix some typos and lint code.

                     Changes in version 0.99.1

  • Internally, a lot of rewritting to remove dplyr usage.

  • Use rlang to control verbosity

  • Fix cases when 2 genes end at the same base before extension

                     Changes in version 0.99.0

  • Initial Bioconductor submission.

BSgenome

                   Changes in version 1.72.0

SIGNIFICANT USER-VISIBLE CHANGES

  • The vignette documenting the seed-based forging process has moved to the BSgenomeForge package. This vignette used to be called the “BSgenomeForge vignette” but it has now be renamed the “Advanced BSgenomeForge usage” vignette.

  • All the tools related to the seed-based forging process and used by the “Advanced BSgenomeForge usage” vignette are now in the BSgenomeForge package.

BSgenomeForge

                    Changes in version 1.4.0

NEW FEATURES

  • Add forgeBSgenomeDataPkgFromTwobitFile()

  • fastaTo2bit() improvement: the function now automatically replaces IUPAC ambiguity letters not supported by the 2bit format with N’s and issue a warning.

SIGNIFICANT USER-VISIBLE CHANGES

  • The vignette documenting the seed-based forging process that used to be in the BSgenome software package is now in the BSgenomeForge package. This vignette used to be called the “BSgenomeForge vignette” but it has now be renamed the “Advanced BSgenomeForge usage” vignette.

  • All the tools related to the seed-based forging process and used by the new “Advanced BSgenomeForge usage” vignette are now in the BSgenomeForge package.

bugsigdbr

                    Changes in version 1.8.2
  • Uniform first-letter capitalization for Body site and Condition terms

CAMERA

                   Changes in version 1.59.1

BUG FIXES

  • Add multtest to dependencies to fix testing on daily build

canceR

                   Changes in version 1.36.5

  • fix issues with indexing Id of Cases and Genetic Profiles

  • Update functionnnalities of GSEA

  • add an example of GCT and CSL fiiles to use in GSEA

  • fix phenoTest analysis

                     Changes in version 1.36.4

  • modify getCases(), getGenProfs()

  • fix get Clinical data

  • fix get Mutation data

  • fix get specific mutation

  • fix get methylation data

  • fix get Profile Data for a single gene

                     Changes in version 1.36.3

  • update welcome panel. get all studies

                     Changes in version 1.36.2

  • Start migration to the new WebAPI of cBioPortal

Cardinal

                    Changes in version 3.5.6

SIGNIFICANT USER-VISIBLE CHANGES

  • Add optional ‘run’ argument to ‘slice()’

  • Add optional ‘plotly’ support for all plotting methods

                      Changes in version 3.5.5

BUG FIXES

  • Fix bug in ‘selectROI()’ region plot updates

                      Changes in version 3.5.4

NEW FEATURES

  • Re-add support for 3D coordinates and ‘image3D()’

SIGNIFICANT USER-VISIBLE CHANGES

  • Export ‘vizi_style()’ and ‘vizi_engine()’ functions

  • Add ‘check’ argument to ‘readMSIData()’ for uuid+checksum

BUG FIXES

  • Fix bug in plotting PLS/OPLS coefficients

  • Fix removing position columns with ‘coord()<-‘

                      Changes in version 3.5.3

NEW FEATURES

  • Add support for multiple instance learning for ‘PLS()’ and ‘spatialShrunkenCentroids()’ with ‘bags’ argument

  • Add ‘estimateReferenceMz()’ for more easily estimating profile m/z-values from ‘MSImagingArrays’

BUG FIXES

  • Make sure ‘bin()’ still respects ‘resolution’ when ‘ref’ is specified (in which case the range is taken from ‘ref’)

  • Fix ‘crossValidate()’ for multiple instance learning

                      Changes in version 3.5.2

BUG FIXES

  • Fix passing ‘tolerance’ in ‘peakProcess()’ when not needed

  • Fix bugs in ‘selectROI()’ not updating the plot

  • Fix bugs in ‘selectROI()’ selecting wrong pixels

  • Make sure ‘peakAlign()’ produces similar results when re-aligning peaks with the same tolerance

                      Changes in version 3.5.1

NEW FEATURES

  • Ground-up rewrite to take advantage of matter v2.5 features

  • New class ‘SpectraArrays’ for arrays of spectra

  • New class ‘SpectralImagingData’ for spectral imaging data

  • New class ‘SpectralImagingArrays’ for raw spectra

  • New class ‘SpectralImagingExperiment’ for centroided spectra

  • New class ‘MSImagingArrays’ for raw mass spectra

  • Updated class ‘MSImagingExperiment’

  • Updated class ‘XDataFrame’

  • Updated classes ‘PositionDataFrame’ and ‘MassDataFrame’

  • New apply method ‘spectrapply()’

  • New processing method ‘recalibrate()’

  • New processing method ‘bin()’

  • New processing method ‘peakProcess()’

  • New classes ‘SpatialResults’ and ‘ResultsList’

  • Updated spatial methods ‘findNeighbors()’ and ‘spatialWeights()’

  • Updated spatial methods ‘colocalized()’

  • Updated projection methods ‘PCA()’ and ‘spatialFastmap()’

  • New projection method ‘NMF()’

  • Updated stats methods ‘PLS()’ and ‘OPLS()’

  • Updated stats method ‘spatialKMeans()’

  • Updated stats method ‘spatialShrunkenCentroids()’

  • Updated stats method ‘spatialDGMM()’

  • Improved visualization methods ‘plot()’ and ‘image()’

SIGNIFICANT USER-VISIBLE CHANGES

  • Deprecated ‘smoothSignal()’ – use ‘smooth()’

  • Deprecated ‘mzBin()’ – use ‘bin()’

  • Deprecated ‘mzAlign()’ – use ‘recalibrate()’

  • Deprecated ‘mzFilter()’ – use ‘subsetFeatures()’

  • Deprecated ‘peakFilter()’ – use ‘subsetFeatures()’

  • Deprecated ‘aggregate()’ – use ‘summarizeFeatures()’

  • Deprecated ‘featureApply()’ – use ‘summarizeFeatures()’

  • Deprecated ‘pixelApply()’ – use ‘summarizePixels()’

               Changes in version 3.4.3 (2023-11-22)

BUG FIXES

  • Fixed default calculation of reference peaks in ‘peakAlign()’

               Changes in version 3.4.2 (2023-11-16)

BUG FIXES

  • Fixed error in ‘readImzML()’ if spectrum representation is missing

  • Fixed bug in ‘writeImzML()’ causing overlapping offsets

               Changes in version 3.4.1 (2023-10-25)

BUG FIXES

  • Fixed bug in ‘writeImzML()’ causing malformed cvParam tag

CardinalIO

                    Changes in version 1.1.6

BUG FIXES

  • Non-existent ‘extraArrays’ produce NULL instead of error

                      Changes in version 1.1.5

BUG FIXES

  • Allow root tags in ‘ImzMeta’ (e.g., if a tag is unknown)

                      Changes in version 1.1.4

SIGNIFICANT USER-VISIBLE CHANGES

  • Updated README.md

                      Changes in version 1.1.3

NEW FEATURES

  • Made ‘writeAnalyze()’ an S4 generic

  • Add optional ‘positions’ parameter to ‘writeAnalyze()’

SIGNIFICANT USER-VISIBLE CHANGES

  • Change ‘writeAnalyze()’ parameter ‘mz’ to ‘domain’

                      Changes in version 1.1.2

BUG FIXES

  • Remove case sensitivity when checking file extensions

                      Changes in version 1.1.1

BUG FIXES

  • Fix error when setting ‘ImzMeta’ elements to NULL

cBioPortalData

                   Changes in version 2.16.0

Bug fixes and minor improvements

  • Improvements to links in documentation and citation section in the vignette

celda

             Changes in version 1.18.2 (2024-04-02)
  • Updated Makevar files to new CRAN standards

  • Fixed unit test causing error

               Changes in version 1.18.1 (2023-11-05)
  • Update to match Bioconductor release version
  • Removed multipanelfigure as a dependency

CellBarcode

                    Changes in version 1.9.1

NEW FEATURES

  • Adding function bc_create_BarcodeObj enabling import processed barcode data
  • a16a9e7 feat: Adding function bc_create_BarcodeObj enabling import process barcode data
  • 45d886a test: adding test for processed data import
  • 1d5f4de doc: add bc_create_BarcodeObj document

FIX

  • Make sure object is data.frame instead of tibble or data.table
  • 895e9a9 fix: make sure the data.frame is pure data.frame instead of tibble or data.table
  • 31e6989 fix: error while checking data.frame

CHORE

  • Error messages and input checks
  • f84b2a1 chore: message if no barcodes found in bulk sequencings
  • e0cded9 chore: Error message when no barcodes are found
  • 3beef87 chore: Check input for sam and bam file

cellxgenedp

                     Changes in version 1.8

SIGNIFICANT USER-VISIBLE CHANGES

  • (v 1.7.2) Add vignette ‘Case studies’, include identifying dataset authors and using ontolgies to identify datasets

  • (v 1.7.1) Update vignette section on dataset visualization to

BUG FIXES

  • (v 1.7.3) Use all collections, datasets, files to determine available columns

ChIPpeakAnno

                   Changes in version 3.37.4

  • Handle the biofilecache error.

                     Changes in version 3.37.3

  • use an updated and unified single vignette to replace the four old ones

  • remove oligoNucleotideEnrichment.R and incorporate it into summarizePatternsInPeaks.R

  • update findMotifsInPromoterSeqs.R to match changes in summarizePatternsInPeaks.R

                     Changes in version 3.37.2

  • export function oligoNucleotideEnrichment

                     Changes in version 3.37.1

  • export disable.logging parameter for venn.diagram called by makeVennDiagram

CircSeqAlignTk

             Changes in version 1.5.2 (2024-04-23)

SIGNIFICANT USER-VISIBLE CHANGES

  • Slot name reversed of CircSeqAlignTkCoverage class was changed to reverse.

NEW FEATURES

  • Add GUI mode. See build_app() for details.

ClassifyR

                    Changes in version 3.8.0
  • Extraction of seed for random number generator fixed.

cleaver

             Changes in version 1.41.3 (2024-04-24)

  • Add 3 different types of trypsin (as defined in PeptideMass): trypsin-high (identical to the current trypsin rule and to PeptideMass’ “higher specificity”), trypsin-low (cleavage after K/R but not if followed by P), trypsin-simple (cleavage after K/R even if followed by P); The trypsin rule is identical to trypsin-high and will be kept for backward compatibility.

               Changes in version 1.41.2 (2023-12-03)

  • Add missing documentation for LysargiNase.

               Changes in version 1.41.1 (2023-11-30)

  • Add LysargiNase cleavage rule.

ClustAll

                   Changes in version 0.99.0
  • Initial release of the ClustAll package for multiple robust stratifications.

clusterExperiment

                   Changes in version 2.23.1
  • Removed option “MB” for argument mergeMethod for the function mergeClusters. This was a method of Meinshausen and Buhlmann (2005) to estimate the number of non-null genes, but their supporting package howmany that implemented the method is no longer supported on CRAN.

clusterProfiler

                   Changes in version 4.10.1
  • bug fixed in parsing KEGG category (2024-03-07, Thu, #664)
  • update citation (#656) and wikipedia data URL (2024-01-10, Wed, #633)

clustifyr

             Changes in version 1.15.2 (2024-04-03)

  • Add support for Seurat version 5 objects

               Changes in version 1.15.1 (2023-10-31)

  • Replace Seurat dependency with SeuratObject

ClustIRR

                   Changes in version 1.1.10
  • New global clustering solution

CompoundDb

                     Changes in version 1.7

Changes in version 1.7.2

  • Import method generics from ProtGenerics.

Changes in version 1.7.1

  • Adapt script to create CompDb from MassBank to new MassBank database format.

consensusSeekeR

                   Changes in version 1.31.2

SIGNIFICANT USER-VISIBLE CHANGES

  • This package now depends on R (>= 3.5.0) because serialized objects in serialize/load version 3 cannot be read in older versions of R.

                     Changes in version 1.31.1

SIGNIFICANT USER-VISIBLE CHANGES

  • The description field of the package is more detailed.

COTAN

                    Changes in version 2.3.6
  • Refactored DEAOnCluster() to make it run faster.
  • Now clustering functions dump the GDI check results for all clusters
  • Changed default GDI threshold to 1.43
  • Added new input to mergeUniformCellsClusters() to allow proper resume of interrupted merges

  • Added possibility to query whether the COEX matrix is available in a COTAN object

                      Changes in version 2.3.5
  • Made checks more strict when adding a clusterization or condition

  • Increased reliability of clustering functions by improved error handling and by allowing retry runs on estimators functions

                      Changes in version 2.3.4
  • Speed-up of GDI calculation via Rfast package
  • Added possibility of using distance between clusters based on Zero-One matrix instead of DEA

  • Added average floor to logFoldChangeOnClusters() to dampen extreme results when genes are essentially absent from a cluster.

                      Changes in version 2.3.3
  • Added method to handle expression levels’ change via log-normalized data: logFoldChangeOnClusters()
  • Minor fix in the import of operators to align to new version of roxigen2

  • Restored default adjustment method of pValueFromDEA() to “none” for backward compatibility reasons

                      Changes in version 2.3.2
  • Solved issue with cleanPlots() when the number of cells exceeded 65536
  • Added methods to calculate the COEX matrix only on a subset of the columns

  • Now the function pValueFromDEA() returns the p-value adjusted for multi-test

                      Changes in version 2.3.1

  • Stopped using explicit PCA via irlba package: using BioConductor PCAtools::pca instead

                      Changes in version 2.3.0
  • First release in Bioconductor 3.19

CRISPRball

             Changes in version 0.99.0 (2023-09-24)
  • Submitted to Bioconductor.

crisprBase

                    Changes in version 1.7.1
  • Updated weights in the SaCas9 nuclease.

crisprDesign

                    Changes in version 1.5.2
  • Added function addReinitiationFlag.

crisprShiny

                    Changes in version 1.0.0
  • New package crisprShiny, for interactive visualizations of GuideSet objects in facilitating the design of CRISPR gRNA.

CTexploreR

                    Changes in version 0.99

CTexploreR 0.99.5

  • Address Bioc review comments.

CTexploreR 0.99.4

  • Don’t run some examples to save time. These functions are illustrated in the vignette.

CTexploreR 0.99.3

  • Reduce check time

CTexploreR 0.99.2

  • Updated unit tests

CTexploreR 0.99.1

  • Addressing the bioconductor comments

CTexploreR 0.99.0

  • Package submission to Biocoductor.

cTRAP

                   Changes in version 1.20.1
  • When running cTRAP(), raise error if commonPath does not exist
  • Fix modular graphical interface functions not showing dropdown choices
  • Update icon names for FontAwesome 6

cypress

            Changes in version 0.99.24 (2024-04-23)

  • update new methods for cedar and deseq2

              Changes in version 0.99.21 (2024-04-06)

  • Coding modified in compliance with BioC requirement.

               Changes in version 0.99.3 (2024-02-12)

  • debug for warning

               Changes in version 0.99.0 (2024-01-15)

  • Submitted to Bioconductor

cytomapper

             Changes in version 1.15.4 (2024-03-21)

  • measureObject fix reversion and test - Bioc 3.19

               Changes in version 1.15.3 (2024-03-13)

  • measureObject fixes for Bioc 3.19 release

               Changes in version 1.15.2 (2023-12-13)

  • change of package maintenance to Lasse Meyer

               Changes in version 1.15.1 (2023-12-10)

  • the unit tests for compImage have now been adjusted to account for correct spillover induction

CytoMDS

                    Changes in version 0.99

CytoMDS 0.99.16

  • added lineWidth parameter in ggplotSampleMDSShepard()
  • running plotly::ggplotly() on ggplotSampleMDSShepard() output now displays row and column number for each distance point.
  • added pointLabelSize and arrowLabelSize in ggplotSample()

CytoMDS 0.99.15

  • corrected bug fix (error message) in pwDist() when verbose=TRUE

CytoMDS 0.99.14

  • re-factored code portions to replace, as much as possible, for loops by apply() family of functions.

CytoMDS 0.99.13

  • re-factored code portions to avoid growing lists incrementally

CytoMDS 0.99.12

  • removed useBiocParallel parameters from various stats functions (use BPPARAM = BiocParallel::SerialParam() as a default)
  • implemented MDS class to store MDS projection results
  • bi-plots now explicitly discard constant external variables (+warning) instead of raising an error without producing a plot
  • implemented ggplotMarginalDensities()
  • updated vignette with Bodenmiller2012 dataset and more biological interpretation.

CytoMDS 0.99.11

  • re-factored package documentation file

CytoMDS 0.99.10

  • biplot now handles extVariables with missing values

CytoMDS 0.99.9

  • in ggplotSampleMDS() : add label layer after geom_point() (no more before)

CytoMDS 0.99.8

  • renamed getChannelSummaryStats() into channelSummaryStats()
  • in channelSummaryStats(), added support for BiocParallel`, and allowed for not loading the whole flowSet in memory at once.
  • replaced NULL defaulted parameters with optional parameters
  • added displayPointLabels argument to ggplotSampleMDS()
  • added displayLegend argument to ggplotSampleMDSWrapBiplots()
  • finalized creating vignette

CytoMDS 0.99.7

  • refactored the pairwise distance calculation code, by pre-computing the unidimensional histograms and store them instead of recalculating them each time a distance between 2 samples is calculated. This improves CPU time and memory consumption.

CytoMDS 0.99.6

  • added subset argument in ggplotSampleMDS() and ggplotSampleMDSWrapBiplots

CytoMDS 0.99.5

  • renamed getPairwiseEMDDist() into pairwiseEMDDist()
  • in pairwiseEMDDist(), added support for BiocParallel, and allowed for not loading the whole flowSet in memory at once.

CytoMDS 0.99.4

  • in getPairwiseEMDDist(), added a second flowSet argument. When the two flowSet arguments are non-null, distances are calculated for all sample pairs, where the first element comes from fs, and the second element comes from fs2.
  • renamed ggplotSamplesMDS into ggplotSampleMDS
  • renamed ggplotSamplesMDSShepard into ggplotSampleMDSShepard
  • renamed getChannelsSummaryStat into getChannelSummaryStats
  • new function ggplotSampleMDSWrapBiplots()

CytoMDS 0.99.3

  • new version of computeMetricMDS() which automatically sets the number of dimensions to reach a target pseudo R squared
  • added ggplotly() functionality for output MDS plots
  • in ggplotSampleMDS(), added flipXAxis, flipYAxis to possibly ease low dimensional projection comparisons
  • in ggplotSampleMDS(), added displayArrowLabels to discard the arrow labels in biplot. Also added arrowThreshold. Moved arrow labels toward the end of the arrows.
  • in ggplotSampleMDS() and ggplotSampleMDSShepard(): added displayPseudoRSq parameter.

CytoMDS 0.99.2

  • use global Rsquare as an indicator of quality of projection
  • use %Var explained per axis

CytoMDS 0.99.1

  • in ggplotSamplesMDS(), added parameter pDataForAdditionalLabelling

CytoML

                    Changes in version 3.11

API Changes

  • Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
  • All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
  • Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76)
  • gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo
  • Some updates to how flowjo_to_gatingset searches for FCS files (#77)
  • Add include_empty_tree option to flowjo_to_gatingset to include samples without gates
  • Allow gatingset_to_flowjo to take a path to a GatingSet archive directory
  • Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic
  • Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

  • Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33
  • Handle change to default stringsAsFactors=FALSE in R 4.0
  • Eliminated extra intermediate files left in temp directory during workspace parsing
  • Switch usage of GatingSetList to merge_gs_list
  • Solve some Windows build issues
  • Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser

  • Add CytoML XSD to installation

                      Changes in version 3.10

API Changes

  • Change handling of quad gates according to RGLab/cytolib#16

  • Renaming of methods:

  • openWorkspace -> open_diva_xml, open_flowjo_xml
  • cytobankExperiment -> open_cytobank_experiment
  • cytobank2GatingSet -> cytobank_to_gatingset
  • parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
  • getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups
  • getSamples -> fj_ws_get_samples, diva_get_samples
  • getKeywords -> fj_ws_get_keywords
  • getCompensationMatrices -> ce_get_compensations
  • getTransformation -> ce_get_transformations

  • compare.counts -> gs_compare_cytobank_counts

  • Renaming of classes:

  • divaWorkspace -> diva_workspace

  • flowJoWorkspace -> flowjo_workspace

  • Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

  • Make gatingset_to_cytobank export cytobank ML with attribute namespaces
  • Allow diva_to_gatingset to use compensation matrix from xml
  • Pass … args from cytobank_to_gatingset appropriately down to FCS parser
  • Fix some issues with scaling of gates parsed from Diva workspace (#64)
  • Guard against unsupported transformations being added to GatingSet during Diva parsing
  • Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
  • Fix ported flowUtils::xmlTag to enable self-closing tags
  • Make gating.graphGML lookup tailored gates by FCS name as well as file id
  • Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

CytoPipeline

                     Changes in version 1.3

CytoPipeline 1.3.6

  • execute() now stores the nb of events retained at each pre-processing step, to speed-up collectNbOfRetainedEvents()

CytoPipeline 1.3.5

  • added CITATION file

CytoPipeline 1.3.4

  • in execute(), when cache does already exist, make it clean before executing the pipeline steps (= preventing inconsistent cache upon crash/forced interruption)

CytoPipeline 1.3.3

  • added collectNbOfRetainedEvents() function

CytoPipeline 1.3.2

  • systematically override pData in cache upon execute() to allow running consistently running several times for increasing number of samples
  • sampleFiles<- and pData<-: make sure that order of sample files follow the one of pData rownames if pData exists.
  • added ‘verbose’ argument in estimateScaleTransforms()

CytoPipeline 1.3.1

  • refactored documentation files

CytoPipelineGUI

                     Changes in version 1.1

CytoPipelineGUI 1.1.3

  • re-factored package documentation file

CytoPipelineGUI 1.1.2

  • added CITATION file

CytoPipelineGUI 1.1.1

  • re-factored documentation files

cytoviewer

             Changes in version 1.3.2 (2024-01-05)

  • added pixel resolution option

               Changes in version 1.3.1 (2024-01-04)

  • updated README and added citation file

dar

                   Changes in version 0.99.13

Bug Fixes

  • Remove humann example form data import vignette

                     Changes in version 0.99.10

New Features

  • Reimplementing step_corncob after the return of corncob package to cran

                     Changes in version 0.99.9

Bug Fixes

  • Set workers parameter to 4 in order to avoid issues with BBS builds

                     Changes in version 0.99.8

Improvements

  • Reducing examples computation time

                     Changes in version 0.99.7

Improvements

  • Reducing examples computation time

                     Changes in version 0.99.6

Improvements

  • Suggest using BiocManager::install() to install dar dependencies

                     Changes in version 0.99.5

Improvements

  • Reducing vignettes computation time

                     Changes in version 0.99.4

Improvements

  • Reducing tests and examples computation time

Bug Fixes

  • Fixing bug in Github Actions on Linux with rlang installation.

                     Changes in version 0.99.3

New Features

  • The dar package now accepts both phyloseq class objects and TreeSummarizedExperiment as inputs.
  • The tutorial has been refocused to become a tutorial on how to import biom, qiime, mothur, metaphlan, and humann into TreeSummarizedExperiment and phyloseq class objects.
  • The Recipe and PrepRecipe classes have been introduced, replacing the previous recipe and prep_recipe classes.
  • The subset and filter operations have been updated to allow all steps of the recipe to be defined in a chainable manner.
  • The functions step_filter_by_abundance, step_filter_by_prevalence, step_filter_by_rarity, and step_filter_by_variance have been added to enhance filtering functionality.

Improvements

  • The R version dependency has been updated to 4.4.0.
  • The dependency on data.table has been removed.
  • The re-export of %>% and := has been removed. Now code examples and vignettes use |>.
  • The required_deps function is no longer exported.
  • The package now recommends more commonly used installation methods, such as BiocManager::install() or install.packages().
  • A warning message is now displayed whenever the rarefy = TRUE option is used, informing users that a fixed seed is being used and how it could impact their results.
  • The package coverage has increased to 82.33%.

Bug Fixes

  • Unconventional package installation methods have been avoided, for example, pak::pkg_install.
  • The setting of a seed within a function (run_aldex) has been addressed.

  • The name of the data in the R/data.R documentation has been corrected from NA.

                     Changes in version 0.99.0
  • Initial Bioconductor submission.

deepSNV

             Changes in version 1.99.3 (2013-07-25)

Updates

  • A few changes to shearwater vignette

  • Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

  • Fixed bug in bf2Vcf() when no variant is called

               Changes in version 1.99.2 (2013-07-11)

Updates

  • Updated CITATION

  • Added verbose option to bam2R to suppress output

  • Changed mode() to “integer” for value of loadAllData()

Bugfixes

  • Fixed bug when only one variant is called in bf2Vcf()

               Changes in version 1.99.1 (2013-06-25)

Updates

  • Using knitr for prettier vignettes

  • Including shearwater vignette

Bugfixes

  • fixed issues with deletions in bf2Vcf()

  • makePrior() adds background on all sites

               Changes in version 1.99.0 (2013-04-30)

Updates

  • New shearwater algorithm

  • Including VCF output through summary(deepSNV, value=”VCF”)

DegCre

                   Changes in version 0.99.16

  • Added utils to DESCRIPTION

                     Changes in version 0.99.15

  • Updated to use R 4.4.0

  • Added importFrom for grDevices and utils

  • Fixed typos in help files

                     Changes in version 0.99.14

BUG FIXES

  • Added imported packages to DESCRIPTION

                     Changes in version 0.99.13

  • Numerous code style changes made to comply with Bioconductor standards.

  • Updated to run require R 4.3.3

  • Vignette style changed to Bioconductor

  • Selective imports implemented

                     Changes in version 0.99.12

BUG FIXES

  • Fixed one more bad href in help files.

                     Changes in version 0.99.11

BUG FIXES

  • Fixed bad hrefs in help files.

                     Changes in version 0.99.10

BUG FIXES

  • Fixed example for runDegCre.

                     Changes in version 0.99.9

BUG FIXES

  • Fixed test functions to subset GRanges.

                     Changes in version 0.99.8

BUG FIXES

  • Fixed runnable examples to load GenomicRanges.

                     Changes in version 0.99.7

BUG FIXES

  • Changed test functions to run on chr1 only for efficiency.

                     Changes in version 0.99.6

BUG FIXES

  • Changed examples to run on chr1 for computational efficiency.

                     Changes in version 0.99.4

BUG FIXES

  • Fixed F to FALSE in example

                     Changes in version 0.99.3

BUG FIXES

  • Set all non-exported functions to not run examples.
  • Fixed vignette code.

NEW FEATURES

  • getAssocDistHits is now exported.

                     Changes in version 0.99.2

BUG FIXES

  • Fixed calcAUC.Rd to not run example.

                     Changes in version 0.99.1

BUG FIXES

  • Fixed calcBinomFDRperBin to give FDR = 1 for 0 assocProbs in top 10 CRE p-values.

                     Changes in version 0.99.0

BUG FIXES

  • Added missing unit test for optimizeAlphaDegCre

DEGreport

                   Changes in version 1.39.4

  • Fix error in check report about stack limit size

                     Changes in version 1.39.3

  • Add ctb

                     Changes in version 1.39.1

  • merging changes from 1.38.1

                     Changes in version 1.38.1

  • remove lasso and fdrtools

  • merge https://github.com/lpantano/DEGreport/pull/56

DelayedArray

                   Changes in version 0.30.0

NEW FEATURES

  • rowsum(<DelayedMatrix>)/colsum(<DelayedMatrix>) now acknowledge the current “automatic realization backend” and “automatic BiocParallel BPPARAM”. See ‘?DelayedArray::rowsum’ for more information.

SIGNIFICANT USER-VISIBLE CHANGES

  • Rename supportedRealizationBackends -> registeredRealizationBackends.

  • Slightly modify the behavior of ‘realize(x, BACKEND=NULL)’. See https://github.com/hansenlab/minfi/issues/256

  • Two important changes to matrix multiplication of DelayedMatrix objects.

    1. Now it returns an ordinary matrix by default (before this change an ordinary matrix was returned wrapped in a DelayedMatrix object). The user can change the default behavior by setting an “automatic realization backend”. See ?DelayedArray::%*% for more information.
    2. Better block processing strategy when only one of the two operands is a DelayedMatrix object (or derivative). The new strategy acknowledges the geometry of the physical chunks of the data in the object. This can make a huge difference in some cases. For example, using a subset of the “1.3 Million Brain Cell Dataset” from 10x Genomics: library(HDF5Array) library(ExperimentHub) hub <- ExperimentHub() tenx <- TENxMatrix(hub[[“EH1039”]], group=”mm10”) M <- tenx[ , 1:25000] m <- cbind(runif(ncol(M)), runif(ncol(M))) M %% m Doing ‘M %% m’ now takes 7.6s and uses 1.1Gb of memory, compared to 110s / 3.1Gb before this improvement. Furthermore, the new strategy operates in linear time and at constant memory: with DelayedArray with DelayedArray ncol(M) 0.29.2 < 0.29.2 ——- —————– —————– 12500 4.3s / 1.1Gb 32s / 2.1Gb 25000 7.6s / 1.1Gb 110s / 3.1Gb 50000 13.4s / 1.1Gb 495s / 5.6Gb 100000 24.0s / 1.2Gg 2409s / 9.1Gb Note that the new strategy is implemented in internal helpers DelayedArray:::BLOCK_mult_Lgrid() and DelayedArray:::BLOCK_mult_Rgrid(). When the two operands are DelayedMatrix objects, the old strategy (which is implemented in DelayedArray:::.super_BLOCK_mult()) is still used.

DelayedMatrixStats

                    Changes in version 1.25

DepecheR

             Changes in version 1.19.9 (2024-01-15)
  • Bug fixes

DeProViR

                   Changes in version 0.99.0
  • Submitting the package

DESeq2

                   Changes in version 1.44.0

  • New method for ‘greaterAbs’ in results() which has more power than the original 2014-2023 method. The old method is available as ‘greaterAbs2014’. Suggested by Nikos Ignatiadis

  • Fix from I-Hsuan Lin for the glmGamPoi dispersion estimation where the wrong indexing of the fitted mean matrix was used, which caused a slowdown.

  • Fix from Rasmus Henningsson where the Cook’s distances for the LRT were computed using a rough estimate of the mean, rather than the one from the GLM estimates of the full model. Now Cook’s distances for Wald and LRT should be consistent.

DESpace

                    Changes in version 1.2.1
  • Update to RELEASE_3_18

DExMA

                   Changes in version 1.10.1

  • Improvement of makeHeatmap function

  • Improvement Effects size meta-analysis methods and results

DifferentialRegulation

                    Changes in version 2.0.2

  • Updated from C++11 to C++17

                      Changes in version 2.0.1

  • traceplot added, with functions plot_traceplot and plot_bulk_traceplot. MAJOR UPDATE

dinoR

                   Changes in version 0.99.0
  • initial Bioconductor submission

distinct

                   Changes in version 1.14.5

  • Linux Rfast BUILD error solved

                     Changes in version 1.14.2

  • Updated from C++11 to C++17

                     Changes in version 1.14.1

  • ERROR solved regarind Rfast dependency

dittoSeq

                    Changes in version 1.16
  • Feature Extensions:
    1. Multi-modality functionality: To support visualization of markers from multiple modalities in the same plot, e.g. gene expression by RNA and protein capture by ADT, the mechanics of ‘assay’, ‘slot’, and ‘swap.rownames’ inputs have been expanded, although defaults are unchanged. See the ‘?GeneTargeting’ documentation page for details. For the standard Seurat CITEseq case, set ‘assay = c(“RNA”, “ADT”)’.
    2. ‘dittoDotPlot()’ vars-categories: Added support for categorization of markers, as well as for x and y axes swapping.
  • Provide ‘vars’ as a named list to group markers (list element values) into categories (list element names).
  • New input ‘vars.dir’ controls which axis is used for markers (“x” by default, or “y”).
  • New boolean inputs ‘categories.theme.adjust’ or ‘categories.split.adjust’ can be used to turn off associated automated additions to the ‘theme’ input or ‘split.adjust’ input as well as faceting mechanics, respectively.
    1. ‘dittoDotPlot()’ 3-color scaling: Added support for injecting a midpoint color to the color scale via 2 new inputs.
  • New input ‘mid.color’ acts as the switch, and can be set to the specific strings “ryb”, “rwb”, or “rgb” (g for gray here) for a single-point quick update to use corresponding ColorBrewer inspired scales (effectively updating ‘min.color’ and ‘max.color’ as well). ‘mid.color’ can alternatively be given a color directly for more fine-grain control of colors.
  • New input ‘mid’ controls the data value at which ‘mid.color’ will be used in the scale.
    1. Additional data representation controls for all ‘dittoPlot()’-style plotters, which includes ‘dittoFreqPlot()’:
  • New input ‘boxplot.outlier.size’ allows control of the outlier shape’s size for “boxplot” representations.
  • New input ‘vlnplot.quantiles’ allows addition of lines at requested data quantiles for “vlnplot” representations.
    1. Added a new built in ‘color.method’ style for ‘dittoScatterHex()’ and ‘dittoDimHex()’ plotters:
  • When ‘color.var’ targets discrete data, giving ‘color.method = “prop.<value>”’, where <value> is an actual data level of ‘color.var’-data, will set coloring to represent the proportion of <value> among the ‘color.var’-data of each bin.
    1. New input ‘labels.repel.adjust’ allows finer control of the ‘do.label’ plot addition, via input pass-through to the geom functions underlying labeling. This affects ‘dittoDimPlot()’, ‘dittoScatterPlot()’, ‘dittoDimHex()’, and ‘dittoScatterHex() functions.
  • Bug Fixes:
    1. ‘dittoHeatmap()’: Fixed a bug which blocked provision of ‘annotation_row’ and ‘annotation_colors’ inputs to ‘dittoHeatmap()’ without also generating column annotations via either ‘annot.by’ or direct ‘annotation_col’ provision.
  • Deprecation:
    1. Completed deprecation of ‘dittoHeatmap()’s ‘highlight.genes’ input via removal from the function.
  • Dependency Upkeep (generally invisible to users):
    1. ggplot-v3: Replaced all calls to the deprecated ‘aes_string()’ function with calls to the standard ‘aes()’ function. In cases where mappings are successively built internally to accommodate customization or flexibility, ‘modifyList()’ usage replaces the previous simple ‘list’ and ‘do.call()’ management.
    2. Seurat-v5: When the user’s Seurat package version is 5.0 or higher, conditional code switches expression data retrieval from a call to the reportedly superseded ‘GetAssayData()’ function to the newly supported ‘SeuratObj[[<assay>]][<slot>]’ syntax.

DMRcate

                    Changes in version 3.0.0

  • Full utility for EPICv2 implemented. DMRs can now be called from the new Illumina Infinium MethylationEPIC v2.0 BeadChip same as the usual pipeline, save for replicate probe filtering (mandatory) and remapping of cross-hybridising probes (optional).

  • Annotation package EPICv2manifest is used as a backend for cpg.annotate().

  • A new function, rmPosReps(), gives multiple user options for filtering replicate probes mapping to the same CpG site. The mean can be taken, or, based on Peters et al. (2024) (see documentation), the probe that is most precise or sensitive to methylation change may be selected.

  • Many thanks to Braydon Meyer and Ruth Pidsley for constructive input and beta testing.

                     Changes in version 2.16.1

  • DSS dependency removed

DOSE

                   Changes in version 3.29.2

  • fix bugs in get_ont_info() and get_dose_data(): wrong object name and wrong data type (2023-11-30, Thu)

                     Changes in version 3.29.1

  • mv ‘MPO.db’ and ‘HPO.db’ from ‘Imports’ to ‘Suggests’ and fixed bugs (2023-11-18, Sat)

dreamlet

                   Changes in version 1.1.18

  • bug fix

                     Changes in version 1.1.17
  • new functionality in plotPCA() and outlierByAssay()
  • works on any list, not just dreamletProcessedData

  • allows outlier analysis on residuals

                     Changes in version 1.1.16
  • Feb 8, 2024
  • fix bug in pbWeights()

  • Fix scaling issue in outlierByAssay()

                     Changes in version 1.1.15
  • Feb 5, 2024
  • Fix bug in call to eBayes()

  • in processAssays() pass argument scaledByLib to voomWithDreamWeights()

                     Changes in version 1.1.14
  • Jan 29, 2024
  • fix bug in pbWeights()
  • smaller pseudo variance

  • limit to only expressed genes by adding getExprGeneNames()

                     Changes in version 1.1.13
  • Jan 25, 2024
  • improve error reporting in seeErrors() and documentation
  • update outlier() to compute z-scores. How returns data.frame()

  • add outlierByAssay() and plotPCA()

                     Changes in version 1.1.12
  • Jan 16, 2024

  • compositePosteriorTest() allows exclude set to be NULL

                     Changes in version 1.1.11
  • Jan 16, 2024

  • add meta_analysis()

                     Changes in version 1.1.10
  • Jan 10, 2024
  • stackAssays() now includeds metadata()$aggr_means correctly

  • add compositePosteriorTest()

                      Changes in version 1.1.9
  • Jan 3, 2024

  • use get_metadata_aggr_means() to extract aggr_means when SCE is produced by cbind’ing

                      Changes in version 1.1.8
  • Dec 18, 2023
  • fix issue when no genes pass cutoffs
  • fix issue with aggr_means in aggregateToPseudoBulk()

  • fix bug when rdf is low for all genes

                      Changes in version 1.1.7
  • Dec 10, 2023
  • add plotBeeswarm()
  • add rowWeightedVarsMatrix()
  • bug fixes
  • add isFullRank() check in dreamlet()

  • handle exceptions in run_mash()

                      Changes in version 1.1.6
  • Dec 5, 2023

  • pbWeights() add argument maxRatio

                      Changes in version 1.1.5
  • Nov 28, 2023
  • fix edge cases in pbWeights()

  • cell weights is not default in dreamlet()

                      Changes in version 1.1.4
  • Nov 27, 2023
  • add pbWeights() to compute precision weights for pseudobulk counts

  • extend extractData() and include it in vignette

                      Changes in version 1.1.3
  • Nov 22, 2023
  • add stackAssays()
  • add diffVar()

  • fix getVarFromCounts) so zeta is a mean, not a sum

                      Changes in version 1.1.2
  • Nov 13, 2023

  • computeLogCPM() uses augmentPriorCount()

                      Changes in version 1.1.1
  • bug fix in Bioc 3.18 and devel

edgeR

             Changes in version 4.2.0 (2024-04-28)

  • The new QL pipeline becomes the default for glmQLFit() by setting legacy=FALSE.

  • Add cameraPR method for DGELRT objects.

  • New arguments prior.n and adaptive.span for voomLmFit().

  • New argument robust for diffSpliceDGE().

  • The NEWS.Rd file has been revised to include the date of each version release and to include earlier versions of edgeR.

  • catchSalmon() now detects whether resamples are Gibbs or bootstrap.

  • The catchSalmon help page now explains the columns of the annotation output data.frame.

  • decideTestsDGE() deprecated in favor of decideTests().

eisaR

                   Changes in version 1.15.1
  • Add legacyQLF argument to runEISA (will be passed to edgeR::glmQLFit)

enrichplot

                   Changes in version 1.23.2
  • separate the JC similarity method (2023-12-11, Mon, #265)

  • fix the issue in ridgeplot(showCategory) : support a vector of Description, not ID(2023-12-1, Fri, #193)

                     Changes in version 1.23.1
  • ridgeplot() supports passing a vector of selected pathways via the ‘showCategory’ parameter (2023-11-30, Thu, #193)
  • fix treeplot() to compatible with the current version of ggtree and ggtreeExtra. (2023-10-28, Sat)
  • add clusterPanel.params[[“colnames_angle”]] parameter to set the angle of colnames. (2023-10-28, Sat)

enrichViewNet

                    Changes in version 1.1.2

NEW FEATURES

  • The new function createEnrichMapMultiBasic() enables the creation of enrichment maps with groups from simple designs.

  • The new function createEnrichMapMultiComplex() enables the creation of enrichment maps with groups from complex designs.

SIGNIFICANT USER-VISIBLE CHANGE

  • The vignette contains new sections presenting the new functions createEnrichMapMultiBasic() and createEnrichMapMultiComplex().

                      Changes in version 1.1.1

SIGNIFICANT USER-VISIBLE CHANGE

  • The enrichViewNet workflow figure, in the vignette, has been updated.

ensembldb

                   Changes in version 2.27.1
  • Functions for coordinate mapping gain support for pre-loaded genomic ranges hence enabling parallel processing support (contribution from Boyu Yu).

epialleleR

             Changes in version 1.11.9 (2024-03-21)

  • uses less memory (due to packed SEQ and XM)

               Changes in version 1.11.8 (2024-03-12)

  • stricter filtering in lMHL reports

               Changes in version 1.11.7 (2024-03-05)

  • optimised reporting from long-read data

               Changes in version 1.11.6 (2024-02-29)

  • float and array tags in simulateBam

  • long-read data input (not optimised yet)

               Changes in version 1.11.5 (2024-02-12)

  • RRBS-ready

               Changes in version 1.11.4 (2024-02-11)

  • methylation calls for bsmap

epiregulon

                   Changes in version 0.99.11

  • new function aggregateAcrossCells has been added, which is implemented in c++ and makes run time for calculateP2G much shorter.

                     Changes in version 0.99.5
  • new function addLogFC which adds log fold changes of gene expression to regulons and significance statistics for differential gene expression
  • cellNum argument to calculateP2G set by default to 100 (previously it was 200).

  • in pruneRegulon the check to the uniqueness of gene names has been added.

                     Changes in version 0.99.0

Version number downgraded to 0.99.0 to meet Bioconductor requirements.

epiregulon.extra

                   Changes in version 0.99.16

  • Vignette updated

                     Changes in version 0.99.5
  • Correct duplication error in plotHeatmapRegulon

  • default direction is changed to “any” in getSigGenes

                     Changes in version 0.99.3
  • default direction is changed to “any” in findDifferentialActivity

  • The previous version regulonEnrich function required at least 3 target genes for a transcription factor to perform geneset enrichment test. Now additional constraint is imposed such that we require at least 3 genes to be present in the geneset.

                     Changes in version 0.99.2

EpiTxDb

             Changes in version 1.15.2 (2024-03-18)
  • Bugfix due to upstream changes in internal functions

erccdashboard

                   Changes in version 1.37.2

BUG FIXES AND MINOR IMPROVEMENTS

  • Added legacy=TRUE for glmQLFit() function from edgeR to maintain behavior equivalent to results with Bioconductor 3.16, rather than using the new method of adjustment for small counts from edgeR that was introduced in Bioconductor 3.18 (legacy = FALSE by default). Changes to the glmQLFit function in edgeR seem to be causing slight changes to dispersion results even with legacy=TRUE.

escape

             Changes in version 1.99.1 (2024-02-29)

UNDERLYING CHANGES

  • ordering by mean values no longer changes the color order
  • add explicit BPPARAM argument to runEscape() and escape.matrix()
  • added additional details in runEscape() and escape.matrix() for make.positive.
  • removed plotting of splitEnrichment() for group.by = NULL

  • separated AUC calculation to rankings and AUC, this was only method found to get consistent scores.

               Changes in version 1.99.0 (2024-02-27)

NEW FEATURES

  • Added runEscape()
  • Added geyserEnrichment()
  • Added scatterEnrichment()
  • Added heatmapEnrichment()
  • Changed enrichIt to escape.matrix()
  • Changed enrichmentPlot to densityEnrichment()
  • performPCA() now works with a matrix or single-cell object
  • pcaEnrichment() combines biplot-like functions

UNDERLYING CHANGES

  • Updated interaction with gsva package
  • Added support for GSVA calculation
  • Added support for AUCell calculation
  • Added support of visualizations and calculations for single-cell objects
  • Modified getGeneSets() to output a list of gene set objects with reformatted names following the Seurat “-“ convention

DEPRECATED AND DEFUNCT

  • Deprecate getSignificance()
  • Deprecate masterPCAPlot()

escheR

                    Changes in version 1.3.1

SIGNIFICANT USER-VISIBLE CHANGES

  • Add functions add_fill_bin and add_ground_bin to provide hexgon binning strategy to mitigate the overplotting of data points
  • Provide an example to use add_fill_bin and add_ground_bin with make_escheR to create hexgon binning plot

esetVis

                   Changes in version 1.29.2

  • interactive plot: replace rbokeh (archived) by plotly

  • doc: use internal keyword for internal functions

                     Changes in version 1.29.1

  • vignette: run rbokeh example only if package is available

EWCE

                   Changes in version 1.11.5

Bug fixes

  • check_bootstrap_args:

  • annotation level for checking cell type names was previous hardcoded to level 1, now updated to match user input for annotation level.

                     Changes in version 1.11.4

Bug fixes

  • drop_uninformative_genes:
  • Will now catch cases where expression matrix is a dataframe and convert to a matrix
  • This was causing weird errors, see issue 92: https://github.com/NathanSkene/EWCE/issues/92

  • Fix made in check_sce() function.

                     Changes in version 1.11.2

New features

  • bootstrap_enrichment_test:
  • New args: standardise_sct_data=, standardise_hits=: let users have more control over data standardisation steps.
  • check_ewce_genelist_inputs: updated accordingly.
  • New arg: store_gene_data to avoid hitting memory limits.

  • Modify test-bootstrap_enrichment_test_2.R to use test new args.

                     Changes in version 1.11.1

Bug fixes

  • ewce_plot() - Dendrogram not reordering cell types in plot
  • see issue
  • Occurs when ctd does not contain the plotting info
  • Fixed now and unit test added.
  • Note that cell type order on the x-axis is based on hierarchical clustering for both plots if make_dendro = TRUE for ewce_plot().

ExperimentHub

                   Changes in version 2.11.0

USER VISIBLE MODIFICATIONS

  • (2.11.2) Update to only install package if interactive and approved by user

BUG FIXES

  • (2.11.3) Herve’s fix. No more call to .get_ExperimentHub() in createHubAccessors() itself, only in the accessor functions that it creates

ExploreModelMatrix

                   Changes in version 1.15.1
  • Add ‘Close app’ button to close the application and export the data

extraChIPs

                    Changes in version 1.7.7

  • Added merge_within to makeConsensus() for better handling when method = “coverage”

                      Changes in version 1.7.6

  • Added the DESeq2 Wald statistic to options for fitAssayDiff()

faers

                   Changes in version 0.99.0
  • Initial Bioconductor submission.

fastreeR

             Changes in version 1.7.3 (2024-04-07)

  • Preparing for next Bioconductor Release.

               Changes in version 1.7.2 (2024-02-10)

  • Fix vignette bug.

               Changes in version 1.7.1 (2024-02-10)

  • Update R version requirement.

               Changes in version 1.7.0 (2023-10-29)

  • Bump x.y.z version to odd y following creation of RELEASE_3_18 branch.

fenr

                   Changes in version 1.0.10
  • Due to recurring issues with build and check on Bioconductor’s machines, I have removed all database downloads from the vignette. Any glitch in the GO server, or simply an internet problem would cause the vignette build to crash. The GO-term information is now attached as data and loaded in the vignette.
  • Made sure the package passes BUILD and CHECK with no internet connection.

  • Correction in vignette: using yeast genome for topGO, instead of human (somehow it was not applied in 1.0.5).

                      Changes in version 1.0.9
  • Changed the way assert_url_path() handles some remote files - it turns out every time it was called, the entire file was unnecessary downloaded, leading to duplication. Now we only assert top directories. Should speed things up!

  • Increased default timeout to 30 s.

                      Changes in version 1.0.8
  • Further improving error handling, making sure assert_url_path() handles timeouts properly

  • Introduced on_error = “ignore” for test purposes

                      Changes in version 1.0.7

  • Improved error handling with unresponsive servers - timeouts are now handled gracefully

                      Changes in version 1.0.6
  • Changed the Ensembl mapping file downloaded from Reactome to “Physical entity” mapping, as it contains gene symbols, in addition to the Ensembl IDs.
  • Changed the name of GAF column DB Object Synonym from gene_synonym to gene_id for consistency with other methods.
  • Corrected Reactome test as it failed with multiple gene symbols per gene id.

  • Replaced biomaRt with a single RESTful XML call; as biomaRt is used only once to obtain GO terms, this replacement reduced dependency footprint of the package

                      Changes in version 1.0.5
  • Bug fix: if feature id - term id mapping is not unique (which can happen), features are duplicated in counting; fixed by dplyr::distinct() on mapping
  • Correction in vignette: using yeast genome for topGO, instead of human.

  • Improving test coverage

                      Changes in version 1.0.4
  • Reinstated Bioplanet access, this time with graceful fail when the website is down.

  • Minor code changes.

                      Changes in version 1.0.2

  • Bug fixes, examples need on_error = “warn”

                      Changes in version 1.0.1
  • First update after Bioconductor release
  • Implemented changes to prevent the package from build/check fail, if one of the remote servers is not responding
  • Moved from httr to httr2
  • Tests and examples now generate warnings in case of server failure
  • Added tests for behaviour in case of a non-responsive server
  • Extended test coverage to 100%, except for the interactive example

findIPs

                   Changes in version 0.99.3

SIGNIFICANT USER-VISIBLE CHANGES

o Format News

                   Changes in version 0.99.2

NEW FEATURES

o Update R version dependency from 4.0.0 to 4.4.0

o Use more importFrom()

BUG FIXES

o Correction on sumRanks()

SIGNIFICANT USER-VISIBLE CHANGES

o Exchange the axis in plotRankScatters()

o Include Installation in Vignette

o Some formatting modification

                   Changes in version 0.99.1

SIGNIFICANT USER-VISIBLE CHANGES

o Some formatting modification

fmrs

                    Changes in version 2.0.1

IMPROVEMENTS SINCE LAST RELEASE

  • Non-mixture of regression models are now added to the package.

BUG FIXES

  • Several bugs are fixed.

                      Changes in version 2.0.0

IMPROVEMENTS SINCE LAST RELEASE

  • The package is rewritten using .Call function.
  • The codes for Weibull distribution are improved.

BUG FIXES

  • Several bugs are fixed which caused the results to be different for the same analysis.

fobitools

                   Changes in version 1.11.4
  • Fix bugs in vignettes

FRASER

                    Changes in version 2.0.0

  • Bugfix for contig names containing certain characters

  • Update of the plot functions to support colorring aberrant status based on p values computed on subsets of genes

  • Major update to FRASER2:

  • Introduction of new & more robust splice metric Intron Jaccard Index

  • Only Intron Jaccard Index metric used by default

  • Improved gene level pvalue calculation and internal storage

  • Introduction of option to limit FDR correction to user-defined subsets of genes per sample (e.g. OMIM genes with rare variant)

  • Updated internal pseudocount parameter and default delta Jaccard cutoff

  • Junction filtering adapted to usage of Intron Jaccard Index metric

  • Require min expression of N >= 10 in 25% of the samples

  • Results table:

  • Functionality to flag outliers in blacklist regions of the genome

  • Functionality to annotate the predicted type of aberrantSplicing (e.g. exon skipping, intron retention etc.)

  • Several updates in the plotting functions

  • introduction of manhattan plot functionality

  • possibility to create sashimi plots to visualize read coverage in the bam files for outliers

gDNAx

             Changes in version 1.2.0 (2024-04-27)

USER VISIBLE CHANGES

  • Prompt an error when a 0-byte BAM file is passed as an argument.

  • Added a new filtering strategy based on stranded genomic windows that can be used when input RNA-seq data is stranded.

  • gDNAx objects store now also strandedness estimated values.

  • identifyStrandMode() has been deprecated in favor of strandedness().

  • gDNAdx() can now automatically guess library layout and protocol.

  • Added a new function gDNAtx() that performs filtering with the most common default strategy.

BUG FIXES

  • Bug fix in the show method for gDNAx objects.

  • Bug fix when the genome() getter on GAlignment* objects is not NA.

gDR

           Changes in version 2024-02-26 (2024-02-26)
  • improve pkgdown site
  • improved references

  • valid NEWS.md

             Changes in version 2024-02-12 (2024-02-12)

  • make documentation compatible with pkdgdown

             Changes in version 2024-01-22 (2024-01-22)

  • add new description fields

             Changes in version 2024-01-19 (2024-01-19)

  • update package vignette

             Changes in version 2023-11-22 (2023-11-22)

  • sync main with devel branch

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-10-18 (2023-10-18)

gDRcore

           Changes in version 2024-04-23 (2024-04-23)

  • add vignette with documentation for data annotation

             Changes in version 2024-04-22 (2024-04-22)

  • add support for external annotation specified in the env var

             Changes in version 2024-03-26 (2024-03-26)

  • fix bug with converting mae into raw_data

             Changes in version 2024-03-15 (2024-03-15)

  • remove unstable tests

             Changes in version 2024-03-14 (2024-03-14)

  • cleanup package

             Changes in version 2024-03-12 (2024-03-12)

  • update function description

             Changes in version 2024-02-26 (2024-02-26)
  • improve pkgdown site
  • improved references

  • valid NEWS.md

             Changes in version 2024-02-14 (2024-02-14)

  • fix issue with retrieving unique records from mix of control and treated samples

  • make documentation compatible with pkdgdown

  • rename ‘matches’ to ‘grr_matches’

             Changes in version 2024-02-12 (2024-02-12)

  • fix unit tests for GRAN

             Changes in version 2024-02-07 (2024-02-07)
  • simplify logic of assays for combination data

  • rename matrix into combination

             Changes in version 2024-02-06 (2024-02-06)

  • add support for internal source of annotation

  • fix bug with converting standardize MAE into raw data

             Changes in version 2024-02-05 (2024-02-05)

  • add vignette for a data model

             Changes in version 2024-02-01 (2024-02-01)

  • update wrappers for co-dilution data

             Changes in version 2024-01-22 (2024-01-22)

  • add new description fields

             Changes in version 2024-01-04 (2024-01-04)

  • improve logic for normalization and identification of single-agent and matrix data with Drug3

             Changes in version 2023-12-15 (2023-12-15)

  • fix issue with wrong assignment of untreated records

             Changes in version 2023-11-22 (2023-11-22)
  • sync master with devel branch
  • add support for unifying duplicates in combo matrix data

  • add “Treatment” as template identifier

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-10-17 (2023-10-17)

gDRimport

           Changes in version 2024-04-08 (2024-04-08)

  • change output of get_exception_data to data.table

             Changes in version 2024-03-26 (2024-03-26)

  • fix issue with reading tsv files

             Changes in version 2024-03-07 (2024-03-07)

  • clean up the package

             Changes in version 2024-02-26 (2024-02-26)
  • improve pkgdown site
  • improved references

  • valid NEWS.md

             Changes in version 2024-02-14 (2024-02-14)

  • make documentation compatible with pkdgdown

             Changes in version 2024-01-22 (2024-01-22)

  • add new description fields

             Changes in version 2023-12-19 (2023-12-19)

  • update package vignette

             Changes in version 2023-12-01 (2023-12-01)

  • update validation function used during data submission

             Changes in version 2023-11-22 (2023-11-22)
  • sync main with devel branch

  • add “Treatment” as template identifier

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-10-17 (2023-10-17)

gDRstyle

           Changes in version 2024-03-25 (2024-03-25)

  • add as_cran flag

             Changes in version 2024-03-20 (2024-03-20)

  • replace remotes:::version_satisfies_criteria function

             Changes in version 2024-03-18 (2024-03-18)

  • temporary skip verifying version test on Bioc

             Changes in version 2024-03-04 (2024-03-04)

  • remove ::: from notes exceptions

             Changes in version 2024-02-26 (2024-02-26)
  • improve pkgdown site
  • improved references

  • valid NEWS.md

             Changes in version 2024-02-12 (2024-02-12)

  • update documentation - pkdown compatibility

             Changes in version 2024-01-16 (2024-01-16)

  • adjust lintr configs

             Changes in version 2023-11-22 (2023-11-22)

  • sync main with devel branch

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-10-17 (2023-10-17)

gDRutils

           Changes in version 2024-04-15 (2024-04-15)

  • add get_testdata_combo and get_testdata_codilution

             Changes in version 2024-03-07 (2024-03-07)

  • clean up the package

  • simplify keywords

             Changes in version 2024-02-28 (2024-02-28)

  • add fit_source to header list

             Changes in version 2024-02-26 (2024-02-26)
  • improve pkgdown site
  • improved references

  • valid NEWS.md

             Changes in version 2024-02-22 (2024-02-22)

  • restore tooltips in table

             Changes in version 2024-02-14 (2024-02-14)

  • make documentation compatible with pkdgdown

             Changes in version 2024-01-30 (2024-01-30)

  • rename matrix into combination

             Changes in version 2024-01-22 (2024-01-22)

  • add new description fields

             Changes in version 2023-12-01 (2023-12-01)
  • fix bug with refining rowData

  • extend the list of headers

             Changes in version 2023-11-22 (2023-11-22)
  • sync master with devel branch
  • update schema to support NA in reference division time
  • add minor fix in code styling
  • add new function gemoetric_mean
  • transform values into numeric in predict_efficacy_from_conc function

  • add “Treatment” as template identifier

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-10-18 (2023-10-18)

GDSArray

                   Changes in version 1.23.1

BUG FIXES

  • Removed gdsfn<- filename setter for GDSArray and GDSArraySeed. Only valid for GDSFile class.

gdsfmt

                   Changes in version 1.38.1

UTILITIES

  • fix the compiler warning: -Wformat-security

GeDi

                   Changes in version 0.99.5
  • This version reflects further changes performed upon the Bioconductor reviewing process.

  • Removed icons from the vignette to reduce the overall size of the package.

                     Changes in version 0.99.4
  • This version reflects the changes performed upon the Bioconductor reviewing process
  • Added col_name_genesets and col_name_genes as parameter to the GeDi() main app to allow users to specify the relevant column names upon executing the command
  • Changes in the R code to comply to best practices (replacing single | with || and similar)
  • Loading the example file does not require anymore the setting of globalVariables()
  • All files retrieved do use some form of caching for avoiding unnecessary re-download operations

  • Reworked the allocation of vectors before for loops to avoid unhealthy growing of vectors/matrices

                     Changes in version 0.99.1

  • The handling of the parallelization for the distance calculations is now unified under the umbrella of BiocParallal, and defaults now to using SerialParam() to avoid unexpected behaviors

                     Changes in version 0.99.0

  • Ready for the submission to Bioconductor!

                     Changes in version 0.90.0
  • Final touches and bug fixes to the main functionality

  • Deployment of the package website via pkgdown

                      Changes in version 0.1.0
  • Officially entering the path of the GeDi!

gemma.R

                    Changes in version 3.0.0
  • Empty outputs now return data.tables with the corresponding column names with 0 rows instead of defaulting to lists of length 0
  • Column names for the outputs of many functions have changed in this release to be more standardized. Please refer to the function documentation. As a general rule names use camelCase separated by .s to indicate properties of a specific entity (eg. experiment.sampleCount) with the exception of acronyms which are always capitalized (experiment.ID)
  • update_results function added which allows re-creation of outputs of gemma.R functions without relying on the original code.
  • get_result_sets function added which allows accessing result sets directly, filtering them based on certain filterable properties (see filter_properties()$resultSet).
  • gemma_memoise function added which allows setting memoisation options without manually setting options
  • get_child_terms function added which returns child terms of an ontology term as inferred by Gemma
  • gemma_kable is added which returns tables formatted to fit

GENESIS

                   Changes in version 2.33.2
  • Set extremely small p-values (< Machine$double.xmin) calculated with pchisq to Machine$double.xmin. This change prevents GENESIS from returning p-values equal to 0.

GeneTonic

                    Changes in version 2.8.0

Other notes

  • Updated functions used from other packages to reflect changes in their API/nomenclature
  • Adapted the internal code of functions to the latest version of igraph - no changes happening for the end user

GenomAutomorphism

                    Changes in version 1.5.1
  • Introducing new functions for DNA and aminoacid sequence representations with physicochemical properties of DNA and aminoacids, which would be useful for further downstream statistical analysis in R.

GenomeInfoDb

                   Changes in version 1.40.0

NEW FEATURES

  • Register the following NCBI assemblies:
    • GRCr8 assembly (Rat)
    • mCavPor4.1 assembly (domestic guinea pig)
    • 21 Escherichia coli assemblies
    • a few Petromyzon marinus (sea lamprey) assemblies

GenomicAlignments

                   Changes in version 1.40.0

NEW FEATURES

  • Add ‘seqinfo’ argument to GAlignments() constructor function.

BUG FIXES

  • mapToAlignments() S at start 0 coordinate fix. By Fedor Bezrukov. See https://github.com/Bioconductor/GenomicAlignments/pull/34

  • Bugfix in isCompatibleWithSkippedExons() for single-end read alignments w/ more than 3 junctions. By Robert Castelo. See https://github.com/Bioconductor/GenomicAlignments/pull/32

GenomicDataCommons

                   Changes in version 1.28.0
  • Defunct legacy function, methods, endpoints, and arguments

GenomicFeatures

                   Changes in version 1.56.0

NEW FEATURES

  • Add getTerminatorSeq(). Same as getPromoterSeq() but for terminator sequences.

SIGNIFICANT USER-VISIBLE CHANGES

  • The makeTxDb*() functions and related have moved to the new txdbmaker package. Full list:
    • makeTxDb
    • supportedUCSCtables
    • browseUCSCtrack
    • makeTxDbFromUCSC
    • getChromInfoFromBiomart
    • makeTxDbFromBiomart
    • makeTxDbFromEnsembl
    • makeTxDbFromGRanges
    • makeTxDbFromGFF
    • supportedUCSCFeatureDbTracks
    • supportedUCSCFeatureDbTables
    • UCSCFeatureDbTableSchema
    • makeFeatureDbFromUCSC
    • supportedMiRBaseBuildValues
    • makePackageName
    • makeTxDbPackage
    • makeTxDbPackageFromUCSC
    • makeFDbPackageFromUCSC
    • makeTxDbPackageFromBiomart Note that they are still temporarily defined in GenomicFeatures but now they just call the corresponding function in txdbmaker. Since this is a temporary redirect, the user also gets a warning that tells them to use the fully qualified name (e.g. txdbmaker::makeTxDbFromUCSC()) to call the function.

GenomicPlot

                   Changes in version 1.1.10

  • Handle NCBI style of seqlevels (seqname)

                      Changes in version 1.1.9

  • Fixed a bug in plot_region

                      Changes in version 1.1.8

NEW FEATURES

  • Add handling of .gz files for bed and bedGraph format.

  • Add input filter for chromosomes. Only specified chromosomes will be included in visualization and analysis.

                      Changes in version 1.1.7

NEW FEATURES

  • Add handle_bedGraph to enable data input of bedGraph format

                      Changes in version 1.1.6

  • Merged a pull request from Hervé Pagès [email protected]

                      Changes in version 1.1.5
  • Added a function to obtain chromosome info from cached data in the ‘circlize’ package to produce a Seqinfo object, which is applied to all GRanges and TxDB object

  • Added another function to generate a customized TxDb object from a genome annotation (GTF or GFF) file.

                      Changes in version 1.1.4

Change chromosome size information source from UCSC web service to cached data in the ‘circlize’ package, to avoid internet connection issues and web service issues.

                    Changes in version 1.1.3

Increase font size for axis labels, align profile with heatmap

                    Changes in version 1.1.1

Removed some suggests in DESCRIPTION to reduce installation time and size

BUG FIXES

Fixed misalignment between profiles and heatmaps

GenomicRanges

                   Changes in version 1.56.0

NEW FEATURES

  • Add terminators() method, same as promoters() but for terminator regions.

BUG FIXES

  • Small fix in makeGRangesFromDataFrame(). Fix error when: (1) input has zero rows, and (2) has no strand field or ‘ignore.strand’ is TRUE. By Marcel Ramos. See https://github.com/Bioconductor/GenomicRanges/issues/81

GenomicScores

                   Changes in version 2.16.0

USER VISIBLE CHANGES

  • Added support to the latest version v4.0 of gnomAD MAF data, stored in the package MafH5.gnomAD.v4.0.GRCh38.

  • Updated vignette to showcase the use of pathogenicity score sets from AlphaMissense, as well as the latest gnomAD v4.0 MAF data.

BUG FIXES

  • Bugfix in ‘getGScores()’ to properly handle resource license information.

GeomxTools

                    Changes in version 3.7.3
  • small bug fix in version comparisons (PKC & Seurat)

  • update SpatialExperiment vignette plot coordinates

                      Changes in version 3.7.2
  • Seurat v5 coercion
  • IPA data loading
  • improved Proteogenomics error handling
  • bug fix on area filtering

gg4way

                    Changes in version 1.1.3

  • Legend improvements

                      Changes in version 1.0.2

  • Improved warning for when genes are not shared by both contrasts

                      Changes in version 1.0.1

  • Minor fix to add support for custom column names to lists of data.frames

ggkegg

             Changes in version 1.1.17 (2024-04-06)

  • stamp function

  • Make some colors non-default in overlay_raw_map

ggsc

                    Changes in version 1.1.4

  • add background outline of umap plot (2024-04-12, Fri, #22)

                      Changes in version 1.1.3
  • support plotting pie for spatial data (2023-12-13, Wed, #18)

  • extract meta.data of Seurat object (2023-12-12, Tue, #17)

                      Changes in version 1.1.2
  • add sc_dot() methods (2023-11-29, Wed, #15)
  • update vignette to link to the online docs (https://yulab-smu.top/ggsc)
  • add README.Rmd and README.md in github repo
  • optimization: retrieve embedding without FetchData (2023-11-27, Mon, #14)

  • bug fixed for Seurat object (2023-10-31, Tue, #12, #13)

                      Changes in version 1.1.1
  • ignore the tissue section when image is not exist (2023-10-31, Tue, #12)
  • introduce joint to combine all features with joint.fun and speed up calculation of kde using RcppParallel (2023-10-25, Wed, #11)

ggspavis

             Changes in version 1.9.1 (2024-03-16)
  • major updates to several plotting functions providing improved flexibility and new features (contributions by Estella Dong)

ggtree

                   Changes in version 3.11.2

  • expose ‘position’ parameter for geom_range() (2024-04-07, Sun, #611)

                     Changes in version 3.11.1

  • copy rect_to_poly() from ggplot2 to make it compatible with ggplot2 3.5.0 (2024-02-13, Tue)

ggtreeExtra

                   Changes in version 1.13.0
  • Bioconductor 3.18 released and Bioconductor 3.19 (devel) version bump. (2023-10-25, Wed)

ggtreeSpace

                   Changes in version 0.99.4
  • address BioC review comments (2024-04-09, Tue, #7-#10)
  • add vignette (2024-03-23, Sat)
  • fixed issues reported by BiocCheck (2024-03-21, Thu)
  • phylospm() (2022-11-22)
  • geom_tsheatmap() (2022-11-18)
  • geom_treeSpace() & ggphylospm() (2022-11-15)
  • ggtreeSpace() to plot phylomorphospace (2022-06-25)

gINTomics

                    Changes in version 1.0.0
  • New package gINTomics, for Multi Omics data integration and visualization

glmGamPoi

              Changes in version 1.15 (2023-11-04)

  • Fix typo in quasi_gamma_poisson_shrinkage example (thanks to @nlubock)

  • Add sample_fraction argument to loc_median_fit (once again thanks @nlubock)

glmSparseNet

                   Changes in version 1.22.0

Breaking changes

  • Adds experiment parameter to different glm* functions.
  • Changing in hashing function to use rlang::hash that reduces a dependency.
  • Deprecates hallmarks function as API has been shutdown.

Miscellaneous

  • Use of native pipe instead of {magritrr}’s %>%
  • Corrects styling and linter issues for better code quality and readability
  • Starts to deprecates parameters using dot.case in favor of camelCase.
  • Increases code coverage to 95%.

GloScope

             Changes in version 1.1.1 (2024-05-01)
  • Added functionality to compute divergence matrix from cell-type proportion vectors

GNOSIS

             Changes in version 1.99.0 (2023-09-04)

  • Made the following significant changes o added functionality to select and upload cBioPortal study o deprecated ability to save R script with executed code

  • Submitted to Bioconductor

GOfuncR

                   Changes in version 1.23.2

USER-LEVEL CHANGES

  • Bugfix for compilation error on Mac

  • Bugfix for refinement “signif” column (see https://github.com/sgrote/GOfuncR/pull/7)

GOSemSim

                   Changes in version 2.29.2

  • update buildGOmap() parameter to consistent with enricher() and GSEA() (2024-02-06, Tue, #47)

                     Changes in version 2.29.1
  • extend godata() to support passing a data.frame (can be output of read.gaf() or read.blast2go()) to ‘annoDb’ (2023-01-16, Tue)
  • deprecate ‘OrgDb’ and introduce new parameter ‘annoDb’ in godata()
  • standardize the output of read.gaf() and read.blast2go()
  • optimize buildGOmap()

GrafGen

             Changes in version 0.99.0 (2024-03-13)
  • Submitted to Bioconductor

GRaNIE

          Changes in version 1.7.3-1.7.4 (2024-04-03)

New features

  • We offer an exciting new feature: Integrating Capture Hi-C or more generally known promoter-enhancer interactions directly into the GRaNIE framework to complement / guide the peak-gene search. For more information, see the Package vignette and the R help for addConnections_peak_gene().
  • Added support for the new JASPAR2024 package and TF motives.

Bug fixes

  • small bug fixes

               Changes in version 1.7.2 (2023-12-08)

Improvements

  • plotPCA_all() now also stores all screeplot and PCA results in the object within GRN@stats$PCA

               Changes in version 1.7.1 (2023-10-26)

  • version jump due to new Bioconductor development cycle

Bug fixes

  • fixed an accidentally recently introduced bug that caused an error in addTFBS when using the JASPAR database
  • made the code more error prone related to AnnotationHub and caching annotation data in cases when the cache directory is corrupted or deleted

graphite

             Changes in version 1.49.1 (2024-04-29)
  • Updated all pathway data.

GreyListChIP

                   Changes in version 1.35.1
  • Added yieldSize argument to countReads method.

GSEABase

                    Changes in version 1.66

SIGNIFICANT USER-VISIBLE CHANGES

  • faster implementation of incidence() for large gene sets / collections (https://github.com/Bioconductor/GSEABase/issues/9)

GSVA

                    Changes in version 1.52

USER VISIBLE CHANGES

  • Moved old API from deprecated to defunct; see vignette and help pages for examples on how to use the new API.

  • Documentation fixes.

  • Gene/feature filtering is not based anymore on floating point arithmetic, but on comparing minimum and maximum values. In the case of expression data stored in dgCMatrix objects, this criterion applies to non-zero values only.

  • Parameter objects have nicer show methods.

  • Resulting enrichment score matrices are now always dense.

  • Added a first version of the support to SpatialExperiment objects. At the moment, only GSVA scores are calculated without using spatial coordinates information.

  • When expression data is stored in an input sparse matrix of class dgCMatrix, now it is handled as such a sparse matrix as much as possible to reduce memory consumption.

  • Added geneSets() and geneSetSizes() methods that allow one to retrieve, respectively, the filtered collection of gene sets and their sizes from either the parameter object or the resulting object output by the gsva() function. This allows the user to more easily give this information to analysis pipelines that exploit it, such as limma-trend; see the vignette for an example.

  • Added functions readGMT() and deduplicateGeneSets() to read GMT files, handling the case when the file contains gene sets with duplicated names; see the corresponding help pages for more information.

  • The underlying code of the ssGSEA method has been optimized after discussion on https://github.com/rcastelo/GSVA/issues/71 and now it runs one order of magnitude faster and consumes one order of magnitude less memory.

BUG FIXES

  • Bugfix on accessing the assay names of a SingleCellExperiment object from the ‘gsva()’ function.

  • Bugfix on a rare combination of input parameter for gsvaParam().

hca

                    Changes in version 1.12

Bug fixes

  • (v. 1.11.1) unlink cache on Bioconductor build system once every 2 weeks to mitigate cache corruption.

  • (v. 1.11.2) manifest() requires modification to accommodate changes introduced by HCA

HDF5Array

                   Changes in version 1.32.0

NEW FEATURES

  • Some light refactoring of the HDF5 dump management utilities:
    • All the settings controlled by the get/setHDF5Dump*() functions are now formally treated as global options (i.e. they’re stored in the global .Options vector). The benefit is that the settings will always get passed to the workers in the context of parallel evaluation, even when using a parallel back-end like BiocParallel::SnowParam. In other words, all the workers are now guaranteed to use the same settings as the main R process.
    • In addition, getHDF5DumpFile() was further modified to make sure that it will generate unique “automatique dump files” across workers.

SIGNIFICANT USER-VISIBLE CHANGES

  • Change ‘with.dimnames’ default to TRUE (was FALSE) in writeHDF5Array().

BUG FIXES

  • Make sure that chunkdim(x) on a TENxRealizationSink, CSC_H5SparseMatrixSeed, or CSR_H5SparseMatrixSeed object ‘x’ always returns dimensions that are at most dim(x), even when ‘x’ has 0 rows and/or columns.

hdxmsqc

                   Changes in version 0.99.3

hdxmsqc 0.99.3

  • updated documentation in response to bioconductor review

hdxmsqc 0.99.1

  • initial version of hdxmsqc package

hermes

                    Changes in version 1.7.1

Enhancements

  • New plotting function draw_heatmap to produce heatmaps of (normalized) counts.

Miscellaneous

  • The utility function df_cols_to_factor now also converts existing factors to having explicit missing levels.
  • Version bump on forcats dependency.
  • Removed ggplot2 deprecation warning ..count…

HIBAG

                   Changes in version 1.40.0

  • new option ‘all’ in hlaUniqueAllele()

                     Changes in version 1.38.3

  • fix compiler warnings: -Wformat & -Wformat-security

  • new ‘use.matching=TRUE’ in hlaPredMerge(); to set ‘use.matching=FALSE’ for backward compatibility

  • ‘ret.postprob=FALSE’ by default in hlaPredMerge()

                     Changes in version 1.38.1

  • fix a compiler warning of “unused-but-set-variable” on Apple ARM chips

  • fix the failure of package loading on Apple ARM chips in the R console

HicAggR

                   Changes in version 0.99.7

  • caching in vignette

                     Changes in version 0.99.6
  • default set column names in OrientateMatrix are now removed, this is for ggAPA
  • ggAPA: “rf” mode has it’s own customized axes labels now

  • added introduction to the package’s vignette

                     Changes in version 0.99.5

  • added option to remove duplicated submatrices in SearchPairs

                     Changes in version 0.99.4

  • removed CITATION file

                     Changes in version 0.99.3
  • NAMESPACE was generated with roxygen2 to define exportable functions.
  • CompareToBackground: to correct the skewedness of o/e values towards long distances, computation of z.scores is now calculated using residuals from a polynomial model that fits the background couples (log(counts)~distance).
  • SearchPairs: added option to remove self interacting bins.
  • all internal functions are now in utilities.R.

  • Docs were reviewed.

                     Changes in version 0.99.2
  • Implemented import of corrected matrices for data in .hic and cool/mcool format.
  • Implemented import of O/E matrix for data in .hic format.
  • Implemented import of raw data in .h5 format.
  • Added GetInfo function to get info on a hic data (.hic, cool/mcool/h5 formats).
  • Removed dependency to BSDA::z.test in CompareToBackground.
  • Removed dependency to InteractionSet and added it as package to import in NAMESPACE to remove the PackageStartUpMessages.
  • Removed chatty package start up message and replaced it with nicer message.

  • Some BiocCheck NOTES were also takedn into consideration: changing sapply to vapply etc.

                     Changes in version 0.99.1
  • Corrected with Bioconductor’s reviews
  • Added PrepareMtxList, ImportLoops, plotMultiAPA & CompareToBackground functions
  • Corrected bugs on seqlevels consistancy and name column for GRanges objects
  • Encapsulated small and internal functions in utilities.R
  • ExtractSubMatrix has option to remove duplicated submatrices
  • Corrected quantilization operations in Aggregation

  • Corrected over all code with suggestions from BiocCheck

                     Changes in version 0.99.0
  • Submitted to Bioconductor

hoodscanR

                    Changes in version 1.1.2

Fix bugs in test with R4.4

                    Changes in version 1.1.1

Small bug fix:

  • when data have cell_id within the colData.

                      Changes in version 1.1.0

Published in Bioconductor.

HybridExpress

                   Changes in version 0.99.0

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.

hypeR

                    Changes in version 2.0.1
  • Dots plots are now explicitly sized with size_by=c(“genesets”, “significance”, “none”)

iCOBRA

                   Changes in version 1.31.2
  • Added ‘Close app’ button to close the shiny app

IgGeneUsage

                    Changes in version 1.17

  • model expanded for designs with biological replicates

  • model expanded for paired sample designs (also with replicates)

igvShiny

           Changes in version 2024-04-23 (2024-04-23)

  • change file links from igv-data.systemsbiology.net to gladki.pl/igvr

             Changes in version 2024-03-16 (2024-03-16)

  • add shinytest2 for igvShinyDemo-GFF3.R

             Changes in version 2024-03-14 (2024-03-14)
  • fix issues with GFF3 data
  • make igvShiny demo app for GFF3 working
  • update trackName of GFF3 (from URL)

  • udpate path to local GFF3

             Changes in version 2024-02-28 (2024-02-28)

  • add pkgdown content

             Changes in version 2024-02-16 (2024-02-16)
  • fix bug in function loadBamTrackFromLocalData

  • improvge way of loading BAM files - show mismatches

             Changes in version 2024-02-09 (2024-02-09)

  • fix some Bioconductor NOTEs

             Changes in version 2024-02-05 (2024-02-05)

  • fix some Bioconductor NOTEs

             Changes in version 2024-02-04 (2024-02-04)
  • make the first Bioconductor release

imcRtools

             Changes in version 1.9.2 (2023-12-14)

  • maintainer change

               Changes in version 1.9.1 (2023-11-20)

  • Switched from aes_ to .data

  • Initialise SPE and SCE objects with colnames

  • Additional test within binAcrossPixels

infercnv

             Changes in version 1.18.1 (2023-12-01)

  • Update to work with Seurat v5 object changes.

  • New default setting for leiden_resolution now set to “auto” which will very roughly set a resolution value that scales with the number of cells to avoid over splitting subclusters when the number of cells increases.

  • Fix for plotting with dynamic_resolution enabled when the png size limit of cairo is hit to not have parts of the plot that try to be plotted outside the limit.

  • Add useRaster option to plot_per_group method and transfer it plot_cnv calls.

  • Transfer cluster_by_groups option to HMM when running in samples mode to allow running the HMM on “all_observations”.

IRanges

                   Changes in version 2.38.0

NEW FEATURES

  • Add terminators(), same as promoters() but for terminator regions.

iSEE

                   Changes in version 2.15.1
  • Add button ‘Draft out a tour’ to navigation bar.
  • Add button ‘About this data set’ to navigation bar.

iSEEfier

                   Changes in version 0.99.2
  • Addressing the points raised in the Bioc review
  • Better checks of the arguments - more compact and robust

  • Explicitly suggesting the instructions to install potentially missing packages for iSEEnrich()

                     Changes in version 0.99.1

  • Ready for Bioconductor review

                     Changes in version 0.99.0

  • Ready for Bioconductor submission!

                      Changes in version 0.3.0
  • Main functions are equipped with extra parameters determining their behavior

  • Unit test suite is fully in!

                      Changes in version 0.2.0

  • Functions renamed to the final version, in a more matching and descriptive manner

                      Changes in version 0.1.0
  • Initial concept of the package!

iSEEindex

                    Changes in version 1.1.1
  • Add possibility to customise the title of the app.

iSEEu

                   Changes in version 1.15.1
  • Expanded the content of the vignette, to have AggregatedDotPlot() and the MarkdownBoard() panels highlighted

ISLET

                    Changes in version 1.5.1
  • personalized deconvolution methods added.

IsoBayes

                    Changes in version 1.0.1

  • load_data inputs SE objects only

  • Updated from C++11 to C++17

isomiRs

                   Changes in version 1.30.1

  • Add color to PCA plot by isoTop function

  • Fix depreciated dplyr code

  • Many other fixes

kebabs

                   Changes in version 1.37.2

  • changed e-mail address of maintainer

  • updated README.md and formatting of package vignette

  • updated references in documentation

  • fixed registration of API calls to C/C++ routines

                     Changes in version 1.37.1

  • minor changes to C++ source code to avoid warnings related to printf-style format strings

                     Changes in version 1.37.0

  • new branch for Bioconductor 3.19 devel

knowYourCG

                   Changes in version 0.99.0
  • First submission of knowYourCG package to Bioconductor

lemur

                     Changes in version 1.1
  • Make predict function faster and less memory intensive for subset fits.
  • Speed-up internal function get_groups
  • Gracefully handle duplicated column names in colData(fit)
  • Give better error message in test_de if cond(..) is used for a fit that was not specified with a design formula (thanks @MaximilianNuber for reporting)

limma

                   Changes in version 3.60.0

  • The default settings for the small.n and min.span arguments of chooseLowessSpan() have been increased, increasing the chosen span value.

  • New argument adaptive.span for voom(). If TRUE, then chooseLowessSpan() is used to select an optimal span value depending on the number of genes, same as is done for vooma(), voomaByGroup() and voomaLmFit().

  • The plot information saved by voom() when save.plot=TRUE now includes pch and cex plotting character settings.

  • The default span set by vooma() is increased slightly to the value given by chooseLowessSpan(ngenes, small.n=50, min.span=0.3, power=1/3). A new argument legacy.span had been added to optionally restore the old default settings for span for users who want backward compatibility.

  • vooma() argument covariate renamed to predictor.

  • vooma() has been revised in several other ways to match the behavior of voom() more closely. The order of arguments has been adjusted to match voom() and lmFit(). A new argument save.plot has been added similar to the same argument for voom(). Changes to have also been made to the title and xlab for the variance trend plot when predictor is non-NULL.

  • New function voomaLmFit() with the same functionality as vooma() but which automates the estimation of sample weights and intrablock correlation from vooma(). It produces an MArrayLM fit object instead of an EList object. It is the analogous to edgeR::voomLmFit() but for continuous microarray-like data.

  • Edits to the help pages for decideTests(), voom(), voomWithQualityWeights(), vooma() and “11RNAseq”. Example added to the vooma() help page.

  • Add RNA-seq to package description.

  • Add Charity Law, Goknur Giner and Mengbo Li to author list in package description.

limpca

                   Changes in version 0.0.99
  • submitted to bioconductor
  • added the argument lmpDataList to pcaBySvd(), plotLine(), plotScatter(), plotScatterM(), plotMeans(), plotDesign()
  • added the function data2LmpDataList()

lute

                   Changes in version 0.99.0
  • Add testthat unit tests.

MACSr

             Changes in version 1.11.2 (2023-11-20)
  • Upgrade to MACS 3.0.0.

MANOR

                   Changes in version 1.75.2

  • Replace calls to ‘class’ by calls to ‘inherits’.

                     Changes in version 1.75.1

  • Fix minor issues in .Rd files.

MAPFX

             Changes in version 0.99.7 (2024-04-30)

  • Fixed issues on WinOS to pass.

  • Updated the README.md file.

               Changes in version 0.99.1 (2024-04-23)

User Visible Changes

  • Addressed reviewer’s comments, including removing repetition and adding unit tests.

  • Ran examples with 2 cores.

               Changes in version 0.99.0 (2024-03-18)

User Visible Changes

  • Created the MAPFX package.

mastR

                    Changes in version 1.3.6

  • Add bioRxiv citation for mastR package.

                      Changes in version 1.3.5

  • Update function remove_bg_exp() using Gaussian distribution percentiles to replace min-max scaling as relative exppression within each sample.

                      Changes in version 1.3.4

  • Update function sig_gseaplot() to allow more custom arguments for enrichplot::gseaplot2().

                      Changes in version 1.3.3

  • Fix names mismatch problem when passing user-defined contrast matrix to DE analysis functions.

                      Changes in version 1.3.2

  • Update function voom_fit_treat() to allow pass user-defined contrast matrix.

                      Changes in version 1.3.1

  • Remove Matrix version bound.

                      Changes in version 1.2.1

  • Specify Matrix (<= 1.6.1.1) to avoid conflicts between SeuratObject and Matrix 1.6-2. Will fix to update to the latest version in BiocVersion 3.19.

MatrixQCvis

             Changes in version 1.11.7 (2024-04-25)

  • add dplyr:: in front of pull function in vignette to avoid errors

               Changes in version 1.11.6 (2024-04-23)

  • add parameter … to function updateSE that will be passed to SummarizedExperiment::assay within updateSE

               Changes in version 1.11.5 (2024-04-12)

  • set parameter multiplyByNormalizationValue in normalizeAssay To TRUE in shinyQC

               Changes in version 1.11.4 (2024-04-02)

  • add option to display size in dimensionReductionPlot

               Changes in version 1.11.3 (2024-03-20)

  • allow quantile normalisation (method = “quantile”) for assays with columns that contain only NA values

               Changes in version 1.11.2 (2024-03-18)

  • fix warning in normalizeAssay

               Changes in version 1.11.1 (2024-03-15)

  • add parameter multiplyByNormalizationValue in normalizeAssay

matter

                   Changes in version 2.5.22

BUG FIXES

  • Fix y-flipped raster images on non-macOS platforms

                     Changes in version 2.5.21

NEW FEATURES

  • Add new vizi mark ‘image’ for plotting pre-rastered images

  • Add arguments ‘rasterImages’ and ‘rasterParams’ to ‘plot_image()’

                     Changes in version 2.5.20

SIGNIFICANT USER-VISIBLE CHANGES

  • Update ‘trans2d()’ and ‘warp2_trans()’ to support arrays

                     Changes in version 2.5.19

NEW FEATURES

  • Add new vizi mark ‘rules’ for reference lines

                     Changes in version 2.5.18

NEW FEATURES

  • Add support for optional ‘plotly’ graphics output

  • Add ‘vizi_engine()’ for setting the plotting engine

  • Add support for 3D images to ‘plot_image()’

SIGNIFICANT USER-VISIBLE CHANGES

  • Export ‘parse_formula()’ for developer use

BUG FIXES

  • Fix ‘plotly’ error from non-gridded voxels

                     Changes in version 2.5.17

SIGNIFICANT USER-VISIBLE CHANGES

  • Allow passing subplots to ‘as_facets()’ via ‘…’

BUG FIXES

  • Fix ‘rowsweep()’/’colsweep()’ behavior with NA groups

  • Fix ‘cv_do()’ and ‘mi_learn()’ behavior with NA labels

                     Changes in version 2.5.16

SIGNIFICANT USER-VISIBLE CHANGES

  • Add PLS 1-component regressions to ‘opls’ output

  • Add ‘fitted()’ method for ‘opls’

  • Update ‘predict()’ method for ‘opls’

  • Add multiple instance learning support to ‘cv_do()’

BUG FIXES

  • Fix ‘opls_nipals()’ usage with ‘mi_learn()’

  • Fix error setting bags to negative class in ‘mi_learn()’

                     Changes in version 2.5.15

BUG FIXES

  • Use names “MacroRecall”/”MacroPrecision” in ‘cv_do()’

                     Changes in version 2.5.14

NEW FEATURES

  • Add function ‘rocscore()’ for calculating ROC AUC

BUG FIXES

  • Fix bug in ‘mergepeaks()’ merging too aggressively

  • Fix NAs in probability in ‘nscentroids()’

  • Fix formatting for ‘size_bytes()’ when vmem is 0

  • Fix bug in ‘cv_do()’ not processing test set

                     Changes in version 2.5.13

BUG FIXES

  • Fix error in ‘estnoise_filt()’ when all peaks are noise

                     Changes in version 2.5.12

SIGNIFICANT USER-VISIBLE CHANGES

  • Add ‘free’ argument to ‘plot_signal()’ and ‘plot_image()’

  • Add ‘style’ argument to ‘set_par()’

  • Return ‘fitted.values’ from each fold in ‘cv_do()’

  • Add ‘pos’ argument to ‘mi_learn()’ to specify positive class

  • Export ‘chunkify()’ and ‘chunk_writer()’ utilities

  • Export ‘size_bytes()’ constructor

BUG FIXES

  • Improve error messages for invalid plotting options

  • Rescale ‘alpha’ channel for images when ‘enhance=TRUE’

  • Return ‘probability’ component for ‘sgmixn()’

  • Prevent mark ‘boxplot’ from plotting extra axes

  • Fix ‘mi_learn()’ failing for missing values in response

  • Fix ‘plot_image()’ failing for constant opacity if ‘scale=TRUE’

                     Changes in version 2.5.11

NEW FEATURES

  • Add RNG utility functions ‘RNGStreams()’, ‘getRNGStream()’, and ‘setRNGStream()’

  • Add ‘seeds’ argument for parallel-safe RNG for ‘chunk_lapply()’, etc.

  • Add ‘type’ argument to ‘drle’ constructor to allow pure-RLE or sequential encoding

  • Add function ‘sgmixn()’ for fitting multiple spatial Gaussian mixture models in parallel

  • Add vizi marks ‘intervals’ and ‘boxplot’

  • Add ‘predscore()’ for scoring predictions

  • Add ‘cv_do()’ for performing cross-validation

SIGNIFICANT USER-VISIBLE CHANGES

  • Change ‘fitted()’ argument ‘type’ to use “response” (instead of “probability”) for ‘nscentroids’

  • Print methods for models (e.g., ‘pls’, etc.) now truncate output to ‘getOption(“matter.show.head.n”)’

  • Add ‘jitter’ transformation for vizi mark ‘points’, etc.

  • Export ‘avg()’ utility function

BUG FIXES

  • Fix bug in ‘nscentroids()’ predictions

  • Fix error in ‘nscentroids()’ for one-class models

  • Fix error in ‘sgmix()’ caused by singleton classes

  • Pass ‘weights’ argument to ‘distfun()’ in ‘fastmap()’ and ‘nscentroids()’

  • Fix error in ‘plot_image()’ for NA-only images

                     Changes in version 2.5.10

NEW FEATURES

  • Add function ‘peakheights()’

  • Add nearest shrunken centroids (‘nscentroids()’)

  • Add spatial Gaussian mixture model (‘sgmix()’)

  • Add colocalization coefficients (‘coscore()’)

  • Add multiple instance learning (‘mi_learn()’)

SIGNIFICANT USER-VISIBLE CHANGES

  • Rename ‘estres()’ parameter ‘tol.ref’ to ‘ref’

  • Export ‘array_ind()’ and ‘linear_ind()’

  • Add ‘nchunks’ argument to ‘prcomp()’ and ‘pls()’

  • Vectorize ‘predict.pls()’ over ‘k’ argument

  • Set corresponding attributes to NULL when center/scale are FALSE in ‘rowscale()’ and ‘colscale()’

BUG FIXES

  • Fix ‘tolerance()’ returning invalid value for ‘tolerance()<-‘

  • Fix error in ‘peakareas()’ when peak boundaries are NULL

  • Remove duplicate peaks in ‘findpeaks_cwt()’

  • Fix potential infinite loop in ‘binpeaks()’

  • Fix potential incorrect vector lengths in ‘simspec()’

                      Changes in version 2.5.9

BUG FIXES

  • When writing to a file in chunk apply functions, preserve order in file even if chunks are processed out-of-order

                      Changes in version 2.5.8

NEW FEATURES

  • Added scaling functions ‘rescale_rms()’, ‘rescale_sum()’, ‘rescale_ref()’, ‘rescale_range()’, and ‘rescale_iqr()’

                      Changes in version 2.5.7

SIGNIFICANT USER-VISIBLE CHANGES

  • Moved ‘keys’ and ‘keys<-‘ generics to Cardinal

  • Removed ‘chunksize’ and ‘chunksize<-‘ generics

BUG FIXES

  • Fix error with NAs in ‘add_alpha()’

  • Fix flipped x/y coordinates in ‘inpoly()’

                      Changes in version 2.5.6

BUG FIXES

  • Fix error in apply functions when ‘BPPARAM=NULL’

  • Remove zero-height peaks in ‘plot_signal()’

                      Changes in version 2.5.5

NEW FEATURES

  • Added ‘plot_signal()’ and ‘plot_image()’

  • Added new mark ‘vizi_text’

SIGNIFICANT USER-VISIBLE CHANGES

  • Add ‘vizi’ style ‘classic’ for transparent background

  • Implement ‘vm_used()’ for ‘sparse_arr’ objects

  • Implement ‘combine()’ for ‘vizi_plot’ objects

  • Rename ‘plot_facets()’ to ‘as_facets()’

BUG FIXES

  • Fixed RStudio plotting bugs due to ‘par(bg=”transparent”)’

  • Fixed ‘matter_list’ subsetting not subsetting type

  • Fixed ‘vizi_pixels’ issues with y-axis

  • Fixed plotting functions not passing along parameters

  • Handle mixed int/double types in ‘ltob()’ and ‘lttb()’

  • Implement ‘vm_used()’ for ‘sparse_arr’

                      Changes in version 2.5.4

BUG FIXES

  • Improved ‘mergepeaks()’ efficiency

                      Changes in version 2.5.3

BUG FIXES

  • Fixed stack overflow in ‘sparse_mat’ subsetting

  • Fixed ‘mergepeaks()’ failing for missing peaks

                      Changes in version 2.5.2

SIGNIFICANT USER-VISIBLE CHANGES

  • For ‘estres()’, allow ‘tol=NA’ or ‘tol=Inf’

                      Changes in version 2.5.1

BUG FIXES

  • Fixed bug in ‘simspec()’ not respecting ‘units’

  • Enabled calling ‘vizi()’ with no arguments

metabinR

             Changes in version 1.5.1 (2024-04-07)

  • Preparing for next Bioconductor Release.

               Changes in version 1.5.0 (2023-10-29)

  • Bump x.y.z version to odd y following creation of RELEASE_3_18 branch.

MetaboAnnotation

                     Changes in version 1.7

Changes in 1.7.5

  • Add parameter addOriginalQueryIndex to matchSpectra() that allows to add an additional spectra variable to the query Spectra with the index in the original object (issue #114).

Changes in 1.7.4

  • Import setBackend() generic from ProtGenerics.

Changes in 1.7.3

  • Add SingleMatchParam for filterMatches to allow selection of (at most) a single match to a target element for each query element.
  • Add new methods queryVariables and targetVariables to extract the names of variables (columns) of query and target.

Changes in 1.7.2

  • Update the Spectra objects within the package to the new versions.

Changes in 1.7.1

  • Add examples and a section to the vignette explaining the use of createStandardMixes.

MetaboCoreUtils

                    Changes in version 1.11

MetaboCoreUtils 1.11.3

  • Add examples on isotopes (including deuterium) can be used with calculateMass (issue #81)

MetaboCoreUtils 1.11.2

  • Add functions to compute quality check of the data (issue #77

MetaboCoreUtils 1.11.1

  • Add functions to enable linear model-based adjustment of (LC-MS derived) abundance matrices (issue #75).

metaseqR2

             Changes in version 1.15.1 (2024-03-07)

NEW FEATURES

  • None.

BUG FIXES

  • Fixed supported Ensembl annotation versions

methodical

                   Changes in version 0.99.0
  • Submission to Bioconductor

methyLImp2

             Changes in version 0.99.8 (2024-03-16)

  • Fixing parallelization set-up.

               Changes in version 0.99.7 (2024-03-14)

  • Fixing “exportglobals = FALSE” in the vignette.

               Changes in version 0.99.6 (2024-03-14)

  • Fixing “BPPARAM” and “assay” usage.

               Changes in version 0.99.5 (2024-03-05)

  • Add “BPPARAM” argument for BiocParallel parallelization.

  • Add “which_assay” and “overwrite_res” arguments for better manupulation of SummarizedExperiment object.

  • Change license.

               Changes in version 0.99.4 (2024-02-29)

  • Switch to ChAMPdata package for annotation instead of the internal one to save space.

  • Add unit tests.

  • Put splitting the dataset by chromosomes in a separate function.

  • Fix Bioconductor review comments.

               Changes in version 0.99.3 (2023-07-01)

  • Fix notes.

               Changes in version 0.99.2 (2023-06-12)

  • Change vignette example data to SummarizedExperiment.

               Changes in version 0.99.1 (2023-06-01)

  • Change of possible input: either numeric matrix or SummarizedExperiment;

  • Adding independent imputation for different samples groups.

               Changes in version 0.99.0 (2023-05-08)

  • First commit.

MGnifyR

                   Changes in version 0.99.23

Date: 2024-03-04

  • getReturn fix: failed constructing MAE if samples in experiments did not match

                     Changes in version 0.99.20

Date: 2024-02-26

  • searchAnalysis returns now a named vector where names are accession IDs that was fed as input

                     Changes in version 0.99.19

Date: 2024-02-15

  • Fix deprecated mgnify_client function

                     Changes in version 0.99.18

Date: 2024-02-12

  • Last modifications for Biocondutor submission

                     Changes in version 0.99.17

  • Added getData function for fetching raw data from the database

                     Changes in version 0.99.0

  • Support for TreeSummarizedExperiment and MultiAssayExperiment

  • Submitted to Bioconductor

mia

                    Changes in version 1.11

  • loadFromMetaphlan: support strain rank

  • agglomerateByRank: agglomerate tree fix

  • Replace taxonomyTree and addTaxonomyTree with getHierarchyTree and addHierarchyTree

  • splitOn: update rowTree fix

  • perSampleDominantFeatures: add new arguments (n, other.name, complete)

  • loadFromMetaphlan: support “taxonomy” column for specifying taxonomy

  • cluster: Overwrite old results instead of failing

  • getPrevalence: bugfix, if assay contains NA values, it does not end up to NA anymore.

  • getExperimentCrossCorrelation fix: enable using of sampleMap in MAE.

  • Implemented the setTaxonomyRanks function to specify which ranks are recognized as taxonomy ranks.

  • Rename cluster to addCluster

  • rename importers loadFromBiom, loadFromQIIME2, readQZA, loadFromMothur, loadFromMetaphlan, loadFromHumann

  • fix typo in loadFromBiom definition (deprecate file)

  • deprecate subsetSamples, subsetFeatures and subsetTaxa

  • deprecate plotNMDS after moving it to miaViz package

  • rename estimateDivergence to addDivergence

  • Add details to documentation of function agglomerateByPrevalence

miaViz

                    Changes in version 1.11
  • replace addTaxonomyTree with addHierarchyTree after renaming in mia package

MicrobiotaProcess

                   Changes in version 1.15.1
  • fix a bug of mp_import_qiime when sample metadata has - character. (2024-04-12, Fri)

  • update mp_plot_diff_cladogram with tidytree and treeio. (2024-03-26, Tue)

                     Changes in version 1.15.0
  • Bioconductor 3.18 released and Bioconductor 3.19 (devel) version bump. (2023-10-25, Wed)

midasHLA

                   Changes in version 1.11.1
  • Fix bug on hlaToVariable() function that variable would erroneously be named NA.

miloR

             Changes in version 2.0.1 (2023-11-09)
  • Introduce NB-GLMM into Milo 2.0 for random effect variables and modelling dependencies between observations
  • Diagnostic function for checking model separation for experimental variables, i.e. splitting zero from non-zero counts perfectly
  • Vignette describing basic usage of GLMM functions in testNhoods

MIRit

                   Changes in version 0.99.13

A minor fix was made to fix the undefined variables note during R CMD check.

                   Changes in version 0.99.12

This version includes several improvements, including a completely revised vignette where all chunks are evaluated, minor tweaks to default values for differential expression analysis, and some bug fixes to the error bars in the plotDE() function. Other issues, such as artifacts in show methods, lacks in documentation, and dependence in DESCRIPTION, have been addressed too.

                   Changes in version 0.99.11

This new version introduces the possibility of limiting validated targets retrieval from miRTarBase to only those interactions supported by extensive experimental evidence. Moreover, minor fixes were made to the vignette, documentation, and internal data. Finally, some examples have been redefined to reduce checking time.

                   Changes in version 0.99.10

This patch introduces a minor fix for one unit test.

                   Changes in version 0.99.9

With this version, significant p-values originating from functional enrichment analyses now include extreme values. Further, examples have been shortened and unit tests now use smaller datasets.

                   Changes in version 0.99.8

This patch further reduces R CMD check time by limiting unnecessary examples and by using smaller datasets for unit tests.

                   Changes in version 0.99.7

This version introduces parallel computing capabilities for the mirnaIntegration() function. This is particularly useful for Boschloo’s exact test, whose execution is now faster. Moreover, the test suite has been redefined to reduce running times.

                   Changes in version 0.99.6

The testing suite has been redefined to allow different results for different versions of packages employed in differential expression analysis.

                   Changes in version 0.99.5

This update fixes a bug in the batchCorrection() function that prevented the correct use of this function with newer versions of the MultiAssayExperiment package.

                   Changes in version 0.99.4

After the implementation of the IS_BIOC_BUILD_MACHINE variable to the Single Package Builder (SPB), this version bump drives a new build to fix errors during R CMD check on SPB.

                   Changes in version 0.99.3

This version fixes a bug in the topologicalAnalysis() function that prevented the use of a functional progress bar during permutation testing. Moreover, the example for the addDifferentialExpression() function has been updated to reduce its running time.

                   Changes in version 0.99.2

MIRit now allows to filter the pathways used for topological analysis based on the number of nodes.

                   Changes in version 0.99.1

Functional enrichment analyses and TAIPA now use cached databases to reduce running times.

                   Changes in version 0.99.0

Initial version for Bioconductor submission.

miRSM

                Changes in version 1.99.7-1.99.8

  • Improve description <2024-04-05, Fri>

                  Changes in version 1.99.0-1.99.6

  • Add new methods for identifying miRNA sponge modules <2024-02-04, Sun>

                     Changes in version 1.21.1

  • Add sponge module at single-sample level and internal competition sponge module <2024-01-26, Fri>

mitch

                   Changes in version 1.15.5

  • The default number of cores has been set to 1.

  • An issue with contrasts being identical has been resolved.

                     Changes in version 1.15.4

  • A bug with tables in the HTML reports has been fixed.

  • Minor improvements to the gmt_import() function to prevent empty sets.

                     Changes in version 1.15.2

  • A new vignette has been included to demonstrate how to conduct enrichment analysis of profiles generated with HM450K and EPIC arrays.

                     Changes in version 1.15.1

  • A change of the gene aggregation algorithm to allow enrichment analysis of infinium methylation analysis.

mobileRNA

                   Changes in version 0.99.23

  • Improved RNAfeatures function

                     Changes in version 0.99.22

  • Fixed issues in RNAimport function

                     Changes in version 0.99.20

  • Build redo

                     Changes in version 0.99.19
  • Missing connective in RNAfeatures when using repeats variable.

  • Added additional check for RNAsequences methods.

                     Changes in version 0.99.17

  • Corrected ORCID references for authors

  • Amended RNAmobile() to ensure removal of non-zero values
  • Improved look of PCA plot
  • Corrected documentation issue and code disparage in plotHeatmap(), and improved styling.

  • Included calculation of consensus sequence determination option for RNAsequence()

                     Changes in version 0.99.15
  • Alteration of vignette and README
  • Included clean FASTQ files as example data sets
  • Updated R data objects
  • Updated citation & news files
  • Addition of new function called mapRNA()
  • Deletion of RNAloci() and RNAmean() functions
  • Additional parameters to RNAimport() to support mRNA data importation
  • Removed parallel computation in RNAmergeGenomes()

  • Improved documentation of functions and removed inconsistencies.

                     Changes in version 0.99.14

Previous changes

  • Added a NEWS.md file to track changes to the package.
  • RNAconsensus() changed to RNAdicercall()
  • Alterations to RNAdicercall() algorithm, including tie options, altered default tidy method.
  • RNAdicercall() introduced new column “DicerCount” and improved the functionality, specifically the exclude parameter.
  • RNAmobile() introduced new parameter, “threshold”
  • Improved RNAsequences() selection algorithm to consider a threshold value, and handling ties.
  • Improved error calling on functions
  • Added RNAdf2e() function
  • Improvements to plotSamplePCA() and plotHeatmap()
  • Amended RNAmergeAnnotations function to meet requirement
  • Removed unnecessary man files for GFF and FASTA files on remote repo
  • Fixed bug in RNAdistribution() plot, when sample specific
  • Broadened use of RNAattributes() function.
  • Updated vignette
  • Updated RNAdicercall() to allow any dicer-classification (not constricted to 20-24)
  • Converted cat() to message() for user information from functions
  • Amended example data
  • Amended CITATION and NEWs file
  • Altered examples in RNAmergeAnnotations/Genomes functions to prevent examples saving into users directory
  • updates inline with bioconductor requirements
  • Amended RNAmergeGenomes() and RNAmergeAnnotations()
  • Removed lazy loading of package data
  • RNAanalysis() changed name to RNAdifferentialAnalysis()

monaLisa

                    Changes in version 1.9.1
  • adapt dumpJaspar to also work with JASPAR2024

Moonlight2R

                    Changes in version 1.1.2

Summary

  • fixed issue with parallelization in URA

                      Changes in version 1.1.1

Summary

  • added new functionality called GMA (Gene Methylation Analysis)
  • added three new visualization functions in connection with GMA: plotGMA, plotMoonlightMet, plotMetExp
  • updated vignette to contain new functionalities related to GMA
  • updated class testing in all functions
  • resized figures

mosdef

                   Changes in version 0.99.4

  • Added persistent location to the script that generates the data objects

                     Changes in version 0.99.3

  • Working on the size and time constraints for the vignette/package to build and check on the BBS

                     Changes in version 0.99.2

  • Better specification of data objects format and location in the installed folder

                     Changes in version 0.99.1

  • This version contains the newly implemented changes as a response to the Bioconductor review. In brief, this includes:

  • renaming the functions (and parameters) to a more consistent style
  • reduction of the dependencies and runtime of checks/tests
  • more details on the exported data objects, and on the outputs (detailed in the vignette)
  • better structure for the vignette with cross-references among sections
  • modularization of some functions to avoid repetitive code
  • implementation of an API which is already framework-agnostic, to later accommodate e.g. edgeR/limma. Mainly, this implies the renaming of the dds to a more generic de_container, whereas the res_de parameter stays constant.

For a full list of all changes implemented, please refer to the PR on the mosdef repository https://github.com/imbeimainz/mosdef/pull/11/

                   Changes in version 0.99.0
  • Ready for submission to Bioconductor!

MOSim

              Changes in version 2.0 (2023-07-21)
  • Added scMOSim functionality

motifStack

                   Changes in version 1.47.1
  • Update documentation of motifStack function.

motifTestR

                   Changes in version 0.99.0
  • Submitted to Bioconductor

msa

                   Changes in version 1.35.5

  • major update of package help page man/msa-package.Rd

                     Changes in version 1.35.4

  • fixes to account for move of substitution matrices from ‘Biostrings’ to ‘pwalign’ package

                     Changes in version 1.35.3

  • changed e-mail address of maintainer

  • updated README.md and formatting of package vignette

  • updated references in documentation

                     Changes in version 1.35.2

  • update of msaMakevars.win in ClustalW to avoid problems arising from compiling ClustalW with C++ 17: added -std=c++14

                     Changes in version 1.35.1
  • update of some Makevars and Makefiles to avoid compliation issues on FreeBSD
    • minor adaptation in vignette

  • minor fix in src/ClustalOmega/src/RClustalOmega.cpp (bug in Rprintf arg list)

                     Changes in version 1.35.0
  • new branch for Bioconductor 3.19 devel

MSA2dist

             Changes in version 1.7.5 (2024-03-28)

BUG FIXES

  • fixed dnastring2kaks to work with local alignments
  • fixed indices2kaks to work with local alignments
  • fixed cds2codonaln to work with local alignments
  • fixed cdsstring2codonaln to work with local alignments

NEW FEATURES

  • added return.cds parameter to cds2aa for local alignments

               Changes in version 1.7.4 (2024-03-18)

BUG FIXES

  • fixed pal2nal

               Changes in version 1.7.3 (2024-03-14)

BUG FIXES

  • fixed dnastring2kaks to return correct orientation

  • fixed pal2nal to use gap_pos-n_i_codons_added-1

               Changes in version 1.7.2 (2024-03-14)

BUG FIXES

  • fixed pal2nal to cover individual gaps longer than 1

               Changes in version 1.7.1 (2024-03-13)

NEW FEATURES

  • added pal2nal
  • added cdsstring2codonaln
  • added indices2kaks
  • added KaKs Calculator 2.0 example to vignette

CHANGES

  • changed dnastring2kaks to use cdsstring2codonaln function

MsBackendMassbank

                    Changes in version 1.11

Changes in 1.11.2

  • Import method generics from ProtGenerics. This requires ProtGenerics version 1.35.3.

Changes in 1.11.1

  • Remove additional empty line at the end of exported MassBank records (issue #49).

MsBackendMgf

                    Changes in version 1.11

Changes in 1.11.2

  • Import generic methods from ProtGenerics. Requires ProtGenerics version 1.35.3.

Changes in 1.11.1

  • Small runtime improvements in MGF importer.

Changes in 1.11.0

  • Bioconductor 3.19 developmental branch.

MsBackendMsp

                     Changes in version 1.7

Changes in 1.7.3

  • Strip whitespaces in values of comments/header information
  • Support also name:value header pairs in addition to name: value (issue #14).
  • Add support for parallel processing for import from a single (large) MSP file.

Changes in 1.7.2

  • Add additional checks to the format of input MSP files to ensure proper data import.

Changes in 1.7.1

  • Import method generics from ProtGenerics. Requires ProtGenerics version 1.35.3.

MsBackendSql

                     Changes in version 1.3

Changes in 1.3.5

  • Improve input argument check and error message for backendInitialize() for MsBackendOfflineSql.
  • Update documentation adding () to all function names.

Changes in 1.3.4

  • Ensure primary keys from the database are in the correct order for backendInitialize().

Changes in 1.3.3

  • Import method generics from ProtGenerics.

Changes in 1.3.2

  • Add a dedicated setBackend method for MsBackendSql and MsBackendOfflineSql backends (issue #17).

Changes in 1.3.1

  • Add description on the use/advantages of different SQL database systems to the vignette.

MsCoreUtils

                    Changes in version 1.15

MsCoreUtils 1.15.7

  • Add common_path() function.

MsCoreUtils 1.15.6

  • Bump version to force new package build on Bioconductor servers.

MsCoreUtils 1.15.5

  • Add function force_sorted() to adjust a numeric vector to ensure increasing/sorted values.

MsCoreUtils 1.15.4

  • Fix partial argument match (see issue #125).

MsCoreUtils 1.15.4

  • Fix documentation of ndotproduct.

MsCoreUtils 1.15.3

  • Add function breaks_ppm to create a sequence of numbers with increasing difference between elements (defined by parameter ppm).

MsCoreUtils 1.15.2

  • Porting baseline estimation function (see issue 119).

MsCoreUtils 1.15.1

  • Remove impute_mle2() since norm2 has been removed from CRAN (see issue 117).

MsCoreUtils 1.15.0

  • New Bioc devel version

MsDataHub

                     Changes in version 1.3

MsDataHub 1.3.4

  • Update vignette: load Report.Derks2022.plexDIA.tsv and benchmarkingDIA.tsv with latest QFeatures.

MsDataHub 1.3.3

  • Add Report.Derks2022.plexDIA.tsv, plexDIA DIA-NN output from Derks et al. (2022).

MsDataHub 1.3.2

  • Fix path to benchmarkingDIA.tsv on zenodo.

MsDataHub 1.3.1

  • Add benchmarkingDIA.tsv data, contributed by Kristina Gomoryova.

MsExperiment

                     Changes in version 1.5

MsExperiment 1.5.5

  • Add spectraSampleIndex() function.

MsExperiment 1.5.4

  • Fix missing export of filterSpectra.

MsExperiment 1.5.3

  • Add filterSpectra method to allow filtering of Spectra within an MsExperiment while keeping possibly present relationships between samples and spectra consistent.

MsExperiment 1.5.2

  • Add support to read/write sample data from/to a MsBackendSql database (issue #39).

MsExperiment 1.5.1

  • Fix subset with negative indices (issue #37.)

MSnbase

                    Changes in version 2.31

MSnbase 2.31.1

  • Disable nested parallel processing for chromatogram() method.
  • Fix Rd notes.

MSnbase 2.31.0

  • New Bioconductor devel.

                      Changes in version 2.29

MSnbase 2.29.4

  • Move XML to suggests.

MSnbase 2.29.3

  • Remove parts of XML dependency.

MSnbase 2.29.2

  • Use fragmentation functions from PSMatch.
  • Mention R for Mass Spectrometry in start-up message.

MSnbase 2.29.1

  • Check for identical ion header in readMgfData() (see issue 597).

MSnbase 2.29.0

  • New devel

msqrob2

                   Changes in version 1.11.2
  • Fixed issue related to levels of a ridge variable

  • Fixed issue when fitting only one random effect

                     Changes in version 1.11.1
  • Fixed issues related to reference class changes in the models
  • Fixed issue related to colData assay levels
  • Refactored internal code

MultiAssayExperiment

                   Changes in version 1.30.0

Bug fixes and minor improvements

  • Updated CITATION information in the main vignette.

multiGSEA

             Changes in version 1.13.1 (2024-04-26)

  • Utilize by default non-adjusted single-omics p-values for aggregation into a composite p-value. Adjustment for multiple testing will be done on the combined multi-omics p-values.

  • Inlcude legacy option for p-value combination to ensure reproducibility.

multistateQTL

             Changes in version 0.99.1 (2024-04-21)

  • Small tweaks e.g. using seq_along()

  • Changed some arguments to use camelCase instead of snake_case

  • Improved vignette.

               Changes in version 0.99.0 (2024-03-22)

  • Submitted to Bioconductor

MungeSumstats

                   Changes in version 1.11.10

New features

  • Can now pass local chain files for liftover (local_chain in format_sumstats() and liftover()).

                     Changes in version 1.11.9

New features

  • Can now control what columns are checked for missing data (drop_na_cols in format_sumstats()). By default, SNP, effect columns and P/N columns are checked. Set to Null to check all columns or choose specific columns.

                     Changes in version 1.11.7

Bug fix

  • Force no tab indexing when writing removed rows of SNPs. This avoids any issues where missing data causes sort errors.

  • Issue fixed when sorting CHR column based on a format when CHR column is a factor.

                     Changes in version 1.11.6

Bug fix

  • Catch for overflow when NA’s in SNP col for check_no_rs_snp() check with imputation_ind=TRUE.

                     Changes in version 1.11.4

Bug fix

  • Minor fix to get_genome_builds() to help with RAM & CPU usage during unit tests. No change in functionality for end user.

                     Changes in version 1.11.3

Bug fix

  • For LDSC format, rename A1 and A2 as LDSC expects A1 to be the effect column rather than A2 (the opposite to MSS’s default) - see more here. Although, this didn’t seem to make any difference to results in tests, see more here.

                     Changes in version 1.11.2

Bug fix

  • Remove unused argument make_ordered from sort_coords()

  • Issue fixed with check ldsc format wehn compute_n type chosen

                     Changes in version 1.11.1

Bug fix

  • Speed up unit test timing for bioc checks (predominately for linux tests)

mzR

                   Changes in version 2.37.3

  • Fix compilation on Windows/aarch64 (#290), thanks to Tomas Kalibera for the patch

                     Changes in version 2.37.2

  • remove mentions of mzData in the DESCRIPTION, vignette and manual files (support dropped in 2.29.3)

                     Changes in version 2.37.1

  • fix compilation on centOS 7 / R-4.3.1 reported in #286

NanoMethViz

                    Changes in version 3.0.0
  • Breaking change to smoothing strategy in plot_gene(), plot_region(), and plot_granges() to use weighted moving mean instead of loess. This deprecates the span argument in favour of smoothing_window which is defaulted to 2000 bases.
  • Smoothing for various plotting functions was previously performed using loess smoothing, this performed locally weighted linear estimation to create a smoothed line, the span argument controlled the proportion of data used in this smoothing. This parameter was difficult to tune because under a fixed span, the smoothed line became flatter as the plot region grew larger. Internally, NanoMethViz dynamically calculated a span that changed inversely proportional to the width of the plotting region, decreasing the span as the plot region grew. However the calculated span was invisible to users, and it unintuitive to users how to set a span to change the appearance of the plot.
  • Changing the smoothing method to a weighted rolling mean lead to the new smoothing_window argument which represents the window size in bases from which data is used for smoothing around each point. This serves the same purpose as the dynamic calculation done previously, but is set more explicitly and should be more intuitive for users. The default is always 2000, and can be increased to increase smoothness and decreased to decrease smoothness.
  • Breaking change to the appearance of plot_gene() plots, previously the isoform annotation would be restricted to only the gene of interest. It is now changed to follow the same behaviour as plot_region() whereby all isoforms in the region are plotted.
  • Breaking change to the default plotting options for plot_region(), plot_gene() and plot_grange() to plot heatmap by default.
  • Possible breaking change to query_methy(simplify = FALSE), it will now return a list that is the same length as the number of regions queried, where it previously returned nothing if a particular sequence was missing from the tabix.
  • Added gene_anno argument to plot_region() and plot_granges() to control whether gene annotation is plotted.
  • Added plot_violin() function for creating violin plots for samples over specific regions.
  • Added check to remove hard-clipped reads because they may not have matching mod strings.
  • Changed gene annotation to always put label on visible isoforms, previously labels are plotted at the center of isoform.
  • Changed the order of columns when querying from ModBam to be the same as when querying from Tabix, with readname at the end instead of being the second column.
  • Fixed memory leak in bam parsing due to out of bounds access.
  • Fixed crash when CIGAR doesn’t match length of SEQ.

NanoStringNCTools

             Changes in version 1.11.1 (2024-04-10)
  • Remove setting font in vignette

NanoTube

                    Changes in version 1.9.1
  • Corrected a bug in positiveQC(), which caused it to calculate different positive scale factors from normalize_pos_control(); the second was confirmed to be correct.

ngsReports

                    Changes in version 2.5.2

  • Added summariseOverrep()

                      Changes in version 2.5.1

  • Changed method for setting default theme using plotTheme

  • Set factor levels for plotSeqContent for FastpDataList

  • Added line & cumulative plotTypes for plotInsertSize

nipalsMCIA

             Changes in version 1.2.0 (2024-04-26)

Major changes

Minor improvements and bugfixes

  • Clarified the dataset used in the single-cell vignette and reformatted the workflow diagram
  • Removed the final log transformation in the single-cell vignette when saving for MCIA

  • Minor plotting improvements (removed redundancies in legend names, consistency of axis text, etc.)

               Changes in version 1.1.0 (2024-03-21)

Major changes

  • Added BiocFileCache to replace previous method of downloading large SC datasets.

Minor improvements and bugfixes

  • Updated nipals_iter to only use var(gs) to compute the significance of global scores.
  • Added to documentation for predict_gs() warning against use with CPCA deflation.

nnSVG

             Changes in version 1.7.1 (2024-03-08)
  • bug fix for non-SpatialExperiment inputs

OmaDB

             Changes in version 2.19.1 (2024-04-18)
  • fix problem with getGenomePairs function after OMA API change

omicsViewer

              Changes in version 1.7 (2024-03-08)

new functions added:

  • the enriched terms are clustered

  • dose response curve function (test)

ontoProc

                   Changes in version 1.25.0
  • introducing owl operations, relying on reticulate

ORFik

                   Changes in version 1.23.8

SIGNIFICANT USER-VISIBLE CHANGES

  • Implemented a Ribo-seq ORF detector now included

  • Added new export functions for bigwig, covRLE

Organism.dplyr

                   Changes in version 1.32.0

BUG FIXES

orthos

                    Changes in version 1.1.1
  • Upgrade libwebp to address security concerns

OUTRIDER

                   Changes in version 1.22.0

  • Add Manhattenplot functionallity

  • Bugfix in restricting for FDR correction and others (#54 and aa6e56a)

  • Ensure correct injections of outliers (#37)

OutSplice

             Changes in version 1.3.1 (2024-03-06)

  • Removed Repitools annoGR2DF

  • Repitools removed from NAMESPACE and DESCRIPTION files

pathlinkR

                  Changes in version 0.99.380

Lots of updates, including:

  • Updated documentation for data and functions
  • Cleaner vignette
  • Better support for Bioconductor classes

  • Better handling of data loading

                    Changes in version 0.99.352

  • Added value tag to data documentation

                    Changes in version 0.99.350

  • Rewrite of pathwayPlots to be more efficient

                    Changes in version 0.99.332
  • Changed methodology for importing functions

  • Added two new functions for PPI networks: “ppiEnrichNetwork” and “ppiExtractSubnetwork”

                    Changes in version 0.99.317

  • Renamed a number of functions to improve consistency, and make it clear which ones are related and part of the same “workflow”

                    Changes in version 0.99.310
  • Big update to the vignette
  • Update to the README and added in the package hex logo

  • Various function tweaks and minor changes

                    Changes in version 0.99.300

  • Renamed package to pathlinkR

                     Changes in version 0.99.1
  • Prepared for bioconductor submission

pathview

                   Changes in version 1.43.1

  • add org.EcK12.eg.db to Suggests for BioC build check

  • korg now include 9767 KEGG species or 1485 new species beyond 2022.

peakPantheR

             Changes in version 1.17.2 (2024-02-26)

  • update unittest for ggplot2 3.5.0

               Changes in version 1.17.1 (2023-11-04)

  • peakPantheR_quickEIC() to plot EIC from raw files

  • SVG output option for AnnotationDiagnostic summary plot

  • Correct Windows-specific file locking issue when calling MSnbase::spectra() in parallel

Pedixplorer

                   Changes in version 0.99.0
  • Kinship2 is renamed to Pedixplorer and hosted on Bioconductor.
  • Pedigree is now a S4 object, all functions are updated to work with the new class
  • Pedigree constructor now takes a data.frame as input for the Pedigree informations and for the special relationship. The two data.fram are normalized before being used.
  • plot.pedigree support ggplot generation, mark and label can be added to the plot. The plot is now generated in two steps ped_to_plotdf() and plot_fromdf(). This allows the user to modify the plot before it is generated.
  • All documentation are now generated with Roxygen
  • New function available: generate_aff_inds, generate_colors, is_informative, min_dist_inf, normData, num_child, useful_inds
  • All functions renamed to follow the snake_case convention
  • All parameters renamed to follow the snake_case convention
  • All test now use testthat files
  • Vignettes have been updated to reflect the new changes

pgxRpi

             Changes in version 0.99.7 (2023-10-20)

  • Add pgxFilter function to expose all available filters.

               Changes in version 0.99.5 (2023-10-10)
  • Updated data structure for frequency data, transitioning from a simple list to Bioconductor containers.

  • Removed sections on survival analysis and frequency clustering analysis from the vignettes to align with the package’s scope.

               Changes in version 0.99.0 (2023-08-25)
  • Submitted to Bioconductor

phantasus

                   Changes in version 1.23.3

  • Changed a configuration scheme

  • setupPhantasus() now can be used to generate a config

  • Support for remote count files via HSDS

phantasusLite

                    Changes in version 1.2.0

  • Switch to https://alserglab.wustl.edu/hsds remote for default HSDS server

  • Depending on rhdf5client >= 1.25.1 to support ARCHS4 v2.3 files

PhyloProfile

                   Changes in version 1.18.0

  • option to specify version for OrthoDB

                     Changes in version 1.16.5

  • fixed detailed plot when name of a taxon is substring of another

  • show supertaxon names when rotate the profile plot

                     Changes in version 1.16.3

  • fixed clustering method not applied

                     Changes in version 1.16.2

  • check if taxonomy DB exists in cwd instead of r/library

                     Changes in version 1.16.1

  • fixed bug wrong order in detailed plot

  • fixed bug mVar for co-orthologs

Pigengene

            Changes in version 1.29.10 (2023-11-15)

Changes in existing functions

  • More diagnostic messages from scoreCandidates.

               Changes in version 1.29.8 (2023-11-13)

Bug Fixes

  • Using “/” is avoided in determine.modules and learn.bn functions to support running them on Windows. The “toLocal” task in learn.bn() and sbatch() still do not support Windows.

General

  • inst/script/bn.calculation.job.R is added as an example for the bnCalculationJob argument.

               Changes in version 1.29.6 (2023-11-10)

Changes in existing functions

  • Setting toCompact to TRUE in make.decision.tree() has the same effect as NULL.

               Changes in version 1.29.4 (2023-11-09)

Bug Fixes

  • The averaged.network() function now correctly passed test data to the module.heatmap() function.

Changes in existing functions

  • More details on the effect of test data in the documentation of one.step.pigengene() and make.decision.tree() functions. make.decision.tree() returns more information on performance.

PIPETS

             Changes in version 0.99.0 (2023-09-26)
  • Submitted to Bioconductor

PIUMA

                    Changes in version 1.0.0
  • PIUMA has been released!

plotgardener

                    Changes in version 1.9.5

NEW FEATURES

  • plotHicSquare has added yaxisDir parameter for flipping the direction of genomic coordinates on the y-axis.

                      Changes in version 1.9.4

BUG FIXES

  • plotManhattan accommodates GRanges data input.

                      Changes in version 1.9.3

BUG FIXES

  • plotGenes appropriately handles tibble input for geneHighlights.

                      Changes in version 1.9.1

NEW FEATURES

  • plotIdeogram has added flip parameter to allow for flipping the ideogram so the end can be before/above the start.

BUG FIXES

  • plotManhattan pch mapping is compatible when number of data points is less than the number of levels of a colorby column.

                      Changes in version 1.9.0

Version bump for Bioconductor 3.18 release.

PLSDAbatch

                   Changes in version 0.99.3
  • Date: 2023-12-21
  • Text: Debug percentileofscore

  • Details: Debug the function percentileofscore(), thus the generated data frame has rownames and colnames as the input data frame to ensure the operation of function percentile_norm()

                     Changes in version 0.99.2
  • Date: 2023-11-14
  • Text: Updates for Bioconductor
  • Details: Update several documents
  • DESCRIPTION: Add a URL field pointing to the GitHub repository
  • vignettes: Wrap as many texts as possible to a character limit of 80; Use library() calls instead of sapply(); Use TreeSummarizedExperiment package to reshape datasets; Remove colorize()

  • R: Update for() loops; Remove extra ### lines

                     Changes in version 0.99.1
  • Date: 2023-05-26
  • Text: Update Imports

  • Details: Move pheatmap, vegan, Biobase, BiocStyle from Suggests to Imports to ensure the generation of vignette

                     Changes in version 0.99.0
  • Date: 2023-04-03
  • Details: This version is equal to the version 0.2.3 on GitHub (https://github.com/EvaYiwenWang/PLSDAbatch-source-code)

pmp

                   Changes in version 1.15.1
  • fix plots due to breaking changes in ggplot2

PoDCall

             Changes in version 1.11.1 (2023-05-15)
  • Vignette spellcheck

podkat

                   Changes in version 1.35.1

  • changed e-mail address of maintainer

  • updated README.md and formatting of package vignette

  • updated CITATION

  • updated references in documentation

                     Changes in version 1.35.0

  • new branch for Bioconductor 3.19 devel

polyester

                   Changes in version 1.99.3

  • NB function now exported

  • note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                     Changes in version 1.99.2

  • bug fix in fragment generation (last 2 bases of transcript were never sequenced)

POMA

                   Changes in version 1.13.26
  • New POMA theme and colorblind-friendly palette
  • Available sample normalization (sum and quantile)
  • New feature normalization methods
  • Extensive review and improvement of all POMA functions
  • Major documentation updates
  • Rename PomaSummarizedExperiment to PomaCreateObject
  • Auto-recognition of variable types and automatic variable re-labeling in PomaCreateObject
  • Available violin plots with PomaBoxplots
  • New functions PomaPCA and PomaPLS as stand-alone functions from the old PomaMultivariate (deprecated)
  • Other new functions: PomaLM, PomaLMM
  • Post-hoc pairwise comparisons in PomaUnivariate
  • Update tests and vignettes

procoil

                   Changes in version 2.31.1

  • changed e-mail address of maintainer

  • updated README.md and formatting of package vignette

  • updated references in documentation

proDA

                    Changes in version 1.17
  • Check that sigma2 is larger than zero (see #21. Thanks to @elena-krismer)

pRoloc

                    Changes in version 1.43

Changes in version 1.43.2

  • Fix/update dunkley2006param object.

Changes in version 1.43.1

  • Fix syntax in man pages.

Changes in version 1.43.0

  • New devel version

ProtGenerics

                   Changes in version 1.35.4

  • Move backendParallelFactor and backendBpparam and supportsSetBackend generics from Spectra.

                     Changes in version 1.35.3

  • Move backendInitialize, backendMerge, setBackend, isReadOnly, peaksData, peaksData<- and peaksVariables, filterRanges, filterValues, filterPrecursorMzRange, filterPrecursorMzValues, filterProductMzRange, filterProductMzValues generics from the Spectra package.

                     Changes in version 1.35.2

  • Add filterSpectra generic.

                     Changes in version 1.35.1

  • Add filterFeatures generic.

psichomics

                   Changes in version 1.28.1
  • Update GTEx data download based on new URL endpoints
  • Documentation:
  • Update function documentation based on bug fixes below
  • Update license copyright years
  • Bug fixes:
  • Fix deprecated used of size in ggplot2::geom_line
  • Fix inconsistent argument in survfit.survTerms()
  • Fix unit test issues when testing low coverage using random PSI values
  • Update pkgdown and R CMD check automation in GitHub Actions

PSMatch

                     Changes in version 1.7

PSMatch 1.7.2

  • Fix connected component dim names in show().

PSMatch 1.7.1

  • In addFragments() use … to pass parameters to calculateFragments().

PSMatch 1.7.0

  • New Bioc devel.

PureCN

                   Changes in version 2.10.0

NEW FEATURES

  • adjustLogRatio function for adjusting a tumor vs normal coverage ratio for purity and ploidy. Useful for downstream tools that expect ratios instead of absolute copy numbers such as GISTIC. Thanks @tedtoal (#40).

SIGNIFICANT USER-VISIBLE CHANGES

  • Provide interval-level likelihood scores in runAbsoluteCN return object. Thanks @tinyheero (#335).

  • Documentation updates. Thanks @ddrichel (#325).

BUGFIXES

  • Bugfix #296 was not merged into the developer branch and did not make it into 2.8.0.

  • Log ratios not shiften to median of sample medians as intended (#356). Thanks @sleyn.

  • Fixed crash with small toy examples (fewer than 2000 baits, #363)

pwalign

                    Changes in version 1.0.0
  • First version of the package that is ready for general use.

qcmetrics

                    Changes in version 1.41

qcmetrics 1.41.1

  • Fix bug when when setting the env.
  • Remove template reporting argument.

QFeatures

                    Changes in version 1.13

QFeatures 1.13.7

  • Fix filterFeatures() when the filter variable also exists in the global environment (issue #208).

QFeatures 1.13.6

  • Migrate .splitS[C]E() unit test form scp to QFeatures.

QFeatures 1.13.5

  • Reuse readQFeatres() params in readQFeatureFromDIANN().

QFeatures 1.13.4

  • Use DIA-NN example data from MsDataHub in readQFeaturesFromDIANN().

QFeatures 1.13.3

  • Fix is.vector() (see issue #203)
  • readQFeatures() multi-set support (ported from scp::readSCP() - see issue #199).
  • new readQFeaturesFromDIANN() function to import DIA-NN report files (ported from scp::readSCPfromDIANN() - see issue #199).

QFeatures 1.13.2

  • Move the filterFeatures generic method to ProtGenerics.

QFeatures 1.13.1

  • Fix typo in vigette.

qPLEXanalyzer

                   Changes in version 1.21.1
  • Added function coefVar.R to calculate and plot coefficient of variance between all samples in a sample group.

raer

                    Changes in version 1.1.3
  • Fixed bug in smart-seq2 pileup_cells reporting

RaggedExperiment

                   Changes in version 1.28.0

New features

  • Added citation information to the vignette and package. See citation(package = “RaggedExperiment”)

Rarr

                     Changes in version 1.3
  • Added support for using the zstd compression library for reading and writing.

rawDiag

            Changes in version 0.99.25 (2024-02-28)
  • Test
  • add test case for rawDiagServerModule
  • Documentation
  • add Visualization section in vignette
  • add shiny and FAQ section in vignette
  • use EH4547(DIA) and EH3222(DDA) data from tatare pkg
  • add FAQ section in vignette
  • Refactor
  • if trailer information is missing add NA
  • Feature

  • handle “Orbitrap Resolution:” in trailer

              Changes in version 0.99.23 (2024-02-15)

  • pass R CMD check on bioconductor with Status: OK

              Changes in version 0.99.19 (2024-02-14)
  • NAMESPACE
  • renamed read.raw to readRaw
  • Documentation
  • add an Introduction and Installation section in vignette
  • removed commented code that isn’t run
  • Code
  • removed paste cmd in message
  • use the BiocParallel

  • refactor rawDiag shiny application, e.g., buildRawDiagShinyApp returns a shiny::shinyApp object

               Changes in version 0.99.9 (2024-01-05)

  • Add NEWS.md file

               Changes in version 0.99.1 (2023-12-06)
  • refacor existing code https://github.com/fgcz/rawDiag
  • use mono assemplies provides through Bioconductor rawrr package
  • camel case for public plot functions, e.g., rename PlotCycleLoad to plotCycleLoad
  • submit to bioconductor #3251

rawrr

             Changes in version 1.10.1 (2023-11-02)
  • Fix index error #67.

rBLAST

             Changes in version 1.1.1 (2024-04-30)

Changes

  • Added description of how to deal with multi-part databases.

  • Fixed package anchors in man pages.

                      Changes in version 1.1.0

Changes

  • makeblastDB() gained parameters db_name, hash_index and verbose.

  • added has_blast() and made tests, man page code and vignette code conditional.

  • added blast_db_cache() and blast_db_get() to manage downloading BLAST DBs using BiocFileCache.

RCy3

                   Changes in version 2.24.0

  • Use stringi to replace uchardet

  • Add test functions

  • Doc fixes:
    • add “c” to anchor choices
  • Bug fixes:
    • fix setNodePositionBypass to support network and base.url
    • use viridis color palette for continuous mapping, #210

ReactomeGSA

             Changes in version 1.17.3 (2024-02-01)

  • Fixed a bug in vignette showcasing the reanalysis of public data.

               Changes in version 1.17.2 (2023-11-28)

  • Added a set of new functions to support ReactomeGSA’s features to load public datasets.

  • Added a new vignette to showcase how public datasets can easily be loaded using the ReactomeGSA package.

                     Changes in version 1.17.1

  • Fixed vignettes

ReactomePA

                   Changes in version 1.47.1
  • Add a disclaimer in package Description to claim that this package is not affiliated with the Reactome team (2023-11-17, Fri)

recount

                   Changes in version 1.29.1

BUG FIXES

  • Merged a pull request by @hpages which addresses some changes to GenomicFeatures. See https://github.com/leekgroup/recount/pull/24 for details.

recoup

             Changes in version 1.31.1 (2024-03-14)

NEW FEATURES

  • No new features.

BUG FIXES

  • Switched to txdbmaker.

RedeR

                    Changes in version 3.0.0

  • Major code refactoring.

  • Improved readability.

  • Reduced code complexities.

  • Improved compatibility with standard base graphics.

RegEnrich

                   Changes in version 1.13.4
  • Fix a bug in GRN.R
  • Fix a bug in DEA_LRT_DESeq2

  • Move BiocStyle to Imports

                     Changes in version 1.13.1
  • Fix the bug of re-building the vignette on Windows.

rgoslin

                    Changes in version 1.8.0

Please note that this Bioconductor version is based on Goslin version 2.2.0. See the Goslin repository and Goslin C++ repository for more details.

Improvements

  • Added more trivial mediators
  • Added prostglandins
  • Added oxylipins
  • Updated functional groups

Bug Fixes

  • Fixed oxo handling
  • Updated lipid class output for plasmanyl / plasmenyl to allow distinction

rGREAT

                    Changes in version 2.5.2

  • add getGeneSetsFromOrgDb()

                      Changes in version 2.5.1

  • support extending from the whole genes

rhdf5

                   Changes in version 2.48.0

CHANGES

  • R complex types can now be written to HDF5. These will be stored as a compound datatype with two elements (r & i) representing the real and imaginary parts.

  • Functions H5Screate_simple and H5Sset_extent_simple now accept numeric values to the dim and maxdim arguments, allowing the creation of HDF5 dataspaces larger than R’s maximum integer value. (Thanks to @hpages for reporting this and providing a patch https://github.com/grimbough/rhdf5/pull/140).

  • Messages about the presence of INT_MIN in datasets created outside of rhdf5, and how R will convert them to NA have been moved from H5Dread to the high-level h5read function. (See https://github.com/LTLA/scRNAseq/issues/44 for more details).

Bug fixes

  • Corrected an issue where the function prototype for _h5fileLock() differed from the actual implementation.

  • Addressed a bug where fixed length string attributes would be one character shorter than they should be. Backported to rhdf5 2.46.1. (Thanks to Aaron Lun @LTLA for reporting this https://github.com/grimbough/rhdf5/issues/132).

  • Fixed an issue where zero length datasets of uint32, int64 or uint64 datatypes could not be read. This would fail with an error message saying there was not enough memory. Backported to rhdf5 2.46.1. (Thanks to Aaron Lun @LTLA for reporting this https://github.com/grimbough/rhdf5/issues/134).

rhdf5filters

                   Changes in version 1.16.0

CHANGES

  • rhdf5filters no longer sets the HDF5_PLUGIN_PATH environment variable when it is loaded. Instead this is handled by the H5PLprepend() function in rhdf5.

BUG FIXES

  • Fixed issue compiling VBZ filter when R was installed via conda. Backported to version 1.14.1. (Reported in https://github.com/grimbough/rhdf5filters/issues/20)

Rhdf5lib

                    Changes in version 1.26

Bug fixes

  • Updated parts of the bundled HDF5 configure scripts (config.guess & config.sub) which were very old and didn’t recognise Apple arm64 systems when running R installed via conda. (Thanks to @eyalbenda for reporting, https://github.com/grimbough/Rhdf5lib/issues/54) Backported to Rhdf5lib version 1.24.2

  • The configure script has been updated to build from source on Windows/aarch64 architecture, rather than trying to use the unsuitable pre-compiled Windows x64 binaries. Thanks to Tomas Kalibera for the patch.

Rhisat2

                   Changes in version 1.19.2

  • Swap GenomicFeatures dependency for txdbmaker

                     Changes in version 1.19.1

  • Exclude unsupported flags in Makefile for Linux aarch64 platform

  • Make mask2iupac a signed char array

Rhtslib

                    Changes in version 3.0.0

SIGNIFICANT USER-VISIBLE CHANGES

  • Update htslib to 1.18 (was 1.15.1)

RNAmodR

             Changes in version 1.17.1 (2024-03-18)
  • Bugfix due to upstream changes in internal functions

RNAseqCovarImpute

             Changes in version 1.1.4 (2024-04-29)

  • bug fix above where dfs were Inf fixed for df AND df_bayes

               Changes in version 1.1.3 (2024-04-12)

  • fixed bug in get_gene_bin_intervals where all genes were not included in some cases

  • fixed bug where dfs were Inf in cases where information loss due to missingness (lambda) was 0

  • Added MI PCA method where we 1) perform PCA on the log CPM values for all genes, 2) create M imputed datasets where the imputation predictor matrix includes all covariates and the optimum number of PCs to retain (e.g., based on Horn’s parallel analysis or the number of PCs that account for >80% explained variation), 3) conduct the standard limma-voom pipeline on each M imputed dataset, and 4) pool the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values

               Changes in version 1.0.2 (2023-10-26)

  • fixed bug in combine_rubins where sigma values were not properly made into a numeric vector

               Changes in version 1.0.1 (2023-10-26)

  • fixed bug in limmavoom_imputed_data_list_helper function where sigma values were not properly output

rols

                    Changes in version 2.99

CHANGES IN VERSION 2.99.4

  • Typo and references in manual pages.

CHANGES IN VERSION 2.99.3

  • Add orcid.

CHANGES IN VERSION 2.99.2

  • Fix different URI locations (see #42)

CHANGES IN VERSION 2.99.1

  • Fix logical syntax in url.

CHANGES IN VERSION 2.99.0

  • Refactoring to use REST API for OLS4.
  • REST queries now use httr2 instead of superseded httr.
  • The term(s) and property constructors are capitalised as Term(), Terms() and Properties().

ropls

                   Changes in version 1.35.4

  • gg_scoreplot: minor update

                     Changes in version 1.35.2

  • gg_scoreplot: update to handle OPLS models

rRDP

             Changes in version 1.37.3 (2024-03-26)

Changes

  • Updated to the lated RDP Classifier version 2.14 released in August 2023 which contains the bacterial and archaeal taxonomy training set No.19.

Rsubread

                   Changes in version 2.18.0
  • Removed the ‘maxMOp’ parameter from featureCounts.

RTCGAToolbox

                   Changes in version 2.34.0

Significant user-visible changes

  • getReport has been removed from the package.

Bug fixes and minor improvements

  • Remove unnecessary imports e.g., from RCircos.

Rvisdiff

             Changes in version 1.1.1 (2024-02-12)

  • Added SVG exportation for line chart, boxplot and heatmap

  • PNG styles fixed

  • PNG resolution enhanced

  • Addded mouse panning to explore boxplot

S4Arrays

                    Changes in version 1.4.0
  • No changes in this version.

S4Vectors

                   Changes in version 0.42.0

NEW FEATURES

  • Add ‘make.names’ argument to as.data.frame() method for DataFrame. See https://github.com/Bioconductor/S4Vectors/issues/121

SIGNIFICANT USER-VISIBLE CHANGES

  • Document global options ‘showHeadLines’ and ‘showTailLines’.

SAIGEgds

                    Changes in version 2.4.0

  • update seqFitLDpruning()

  • reduce the memory usage in seqAssocGLMM_SPA() when the genotype file is not split by chromosomes

                      Changes in version 2.2.1

  • fix the compiler warning: -Wformat-security

  • fix a compiler issue with gcc v7.5

sangeranalyseR

                    Changes in version 99.1
  • Base class: SangerReads is designed to store each forward/revers reads.

saseR

                   Changes in version 0.99.0

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.

scanMiR

             Changes in version 1.9.3 (2024-02-09)
  • since ggseqlogo was removed from CRAN, it was replaced and the logo plot layouts are slightly different

scAnnotatR

             Changes in version 1.9.2 (2024-04-01)

  • Fixed bug in classify_cells_sce.

               Changes in version 1.9.1 (2024-03-21)

  • Adapted vignettes to address changes in scRNAseq package.

SCArray

                   Changes in version 1.12.0
  • update according to DelayedArray (>= v0.29.0)

SCArray.sat

                    Changes in version 1.4.0
  • update for Seurat v5

scMitoMut

                   Changes in version 0.99.5
  • Update README add biocondutor installing info
  • Make sure the subsetting cells and loc must be unique in scMitoMutObj

  • Add alternative reads count threshold for loc filtering (alt/_count)

                     Changes in version 0.99.2

Initiate package.

scMultiSim

                   Changes in version 0.99.9

Prepare for the Bioconductor release

  • Fix build errors

                     Changes in version 0.99.8

Prepare for the Bioconductor release

  • Tidy up the code, add more comments

                     Changes in version 0.99.7

Prepare for the Bioconductor release

  • Fix build errors

scp

                    Changes in version 1.13

scp 1.13.6

(nothing yet)

scp 1.13.5

  • fix: fixed small error in degrees of freedom
  • fix: break workflow upon infinite values

scp 1.13.4

  • fix: first drop variable before centering numerical variables (see #54)

scp 1.13.3

  • Refactor readSCP() and readSCPFromDIANN() to use new QFeatures implementations.

scp 1.13.2

  • New scplainer workflow and citation
  • Add addReducedDims() (see #52)
  • fix: logFC and associated SE are now correctly computed

scp 1.13.1

  • docs: fixed vignette about reporting missing values
  • docs: add a QFeatures figure to the nutshell vignette

scp 1.13.0

  • New Bioconductor 3.18 (devel) release

scRepertoire

             Changes in version 2.0.0 (2024-01-10)

NEW FEATURES

  • Added percentAA()
  • Added percentGenes()
  • Added percentVJ()
  • Added percentKmer()
  • Added exportClones()
  • Added positionalEntropy()
  • Added positionalProperty()
  • Changed compareClonotypes to clonalCompare()
  • Changed clonotypeSizeDistribution to clonalSizeDistribution()
  • Changed scatterClonotypes to clonalScatter()
  • Changed quantContig to clonalQuant()
  • Changed highlightClonotypes to highlightClones()
  • Changed lengthContigs to clonalLength()
  • Changed occupiedscRepertoire to clonalOccupy()
  • Changed abundanceContig to clonalAbundance()
  • Changed alluvialClonotypes to alluvialClones()
  • Added features to clonalCompare() to allow for highlighting sequences, relabeling clonotypes.

UNDERLYING CHANGES

  • Removed internal .quiet() function.
  • .theCall() now allows for a custom header/variable and checks the colnames.
  • Replaced data arguments to be more descriptive: df is now input.data, dir is now input, and sc is now sc.data
  • Deep clean on the documentation for each function for increased consistency and explainability
  • StartracDiversity() metric re-implemented to remove startrac-class object intermediary
  • Implemented powerTCR locally to reduce dependencies and continue support
  • Universalized underlying function language and intermediate variables
  • License change to MIT
  • group.by and split.by have been consolidated into single group.by parameter
  • Added support for Immcantation pipeline, .json, Omniscope, and MiXCR formats for loadContigs()
  • Made GitHub.io website for support/vignettes/FAQ
  • Restructured NEWS Tracking
  • Added testthat for all exported and internal functions
  • Fixed issue with clonalQuant() for instance of scale = FALSE and group.by being set.
  • clonalDiversity() no longer automatically orders samples.
  • Remove order parameter from clonalQuant(), clonalLength(), and clonalAbundance()
  • x.axis parameter in clonalDiversity() separated from group.by parameter
  • filtering chains will not eliminate none matching chains.

DEPRECATED AND DEFUNCT

  • Deprecate stripBarcodes()
  • Deprecate expression2List() (now only an internal function).
  • Deprecate checkContigs()

scRNAseqApp

                   Changes in version 1.3.25

  • Fix the abstract issue for edit module.

                     Changes in version 1.3.24

  • Update the description.

                     Changes in version 1.3.23

  • Add a hyperlink to package URL at footer.

                     Changes in version 1.3.22

  • Fix the duplicated rownames.

                     Changes in version 1.3.21

  • Add search button in the home page.

                     Changes in version 1.3.20

  • Change the default waffle plot group to celltype.

                     Changes in version 1.3.19

  • Update abstract in the admin edit tab.

                     Changes in version 1.3.18

  • Add abstract parameter for createAppConfig

                     Changes in version 1.3.17

  • Fix the issue if no ip location information available when update from the older version.

  • add the possibility of the feature names to replace the rownames.

                     Changes in version 1.3.16

  • Fix the missmatch UI and ID.

                     Changes in version 1.3.15

  • Fix the no id column issue when update the database.

                     Changes in version 1.3.14

  • Update the maxOptions from 6 to 50.

                     Changes in version 1.3.13

  • Add groupby parameter for correlation for proportion plot.

                     Changes in version 1.3.12

  • Add correlation for proportion plot.

                     Changes in version 1.3.11

  • Add Wilcoxon test for violin plot.

                     Changes in version 1.3.10

  • Add Chisq test for proportion.

                      Changes in version 1.3.9

  • Fix some typos.

                      Changes in version 1.3.8

  • Change dependence from hdf5r to rhdf5.

                      Changes in version 1.3.7

  • Fix the wrong downloader handler in downloader module.

                      Changes in version 1.3.6

  • Add downloader module.

                      Changes in version 1.3.5

  • Add gene name map to sql database.

                      Changes in version 1.3.4

  • Fix the issue of missing stats for cell numbers.

                      Changes in version 1.3.3

  • Add user visit info and gene symbols into the sql database.

                      Changes in version 1.3.2

  • Add dataset configuration into the sql database.

                      Changes in version 1.3.1

  • Make it compatable with SeuratObject V5.

SeqArray

                   Changes in version 1.44.0

UTILITIES

  • tweak the display of progress information in seqVCF2GDS()

  • seqVCF_Header(, getnum=TRUE, verbose=TRUE) to show the progress information for scanning the VCF file

  • new seqGetData(, "$dosage_alt2") and seqGetData(, "$dosage_sp2") for sex chromosomes, when the alleles are partially missing (e.g., genotypes on chromosome X for males)

  • new ‘verbose.clean’ in seqExport() to control how much information to be displayed

                     Changes in version 1.42.4

BUG FIXES

  • seqGetData(, "$dosage_alt") and seqGetData(, "$dosage_sp") work correctly when the ploidy is >2 and there are missing alleles

  • fix a bug that seqParallel() does not call a user-defined ‘.combine’ when ‘parallel=1’

                     Changes in version 1.42.1

UTILITIES

  • update the help files of seqBlockApply() and seqUnitApply()

  • detect the output filename extension in seqGDS2VCF() without considering the case of the characters, supporting .gz, .bgz, .bz and .xz as a filename extension

  • fix the compiler warning: -Wformat-security

  • new option ‘include.pheno=TRUE’ in seqBED2GDS()

shiny.gosling

                   Changes in version 0.99.0
  • Added a NEWS.md file to track changes to the package.

signeR

                    Changes in version 2.5.1
  • Preserve dimnames from the given input matrices

signifinder

                    Changes in version 1.6.0

  • Add 15 new signatures.

  • Update the evaluationSignPlot function to return an overall goodness score.

  • Add getSignGenes function to access the signatures gene list.

  • When multiple signatures are plotted, values are reported in z-scores and not rescaled between 0 and 1 as before.

SimBu

             Changes in version 1.5.3 (2023-11-21)

  • Added ‘seed’ parameter to simulation

               Changes in version 1.5.2 (2023-11-08)

  • Updated SimBu to be compatibel with Seurat v5

simPIC

             Changes in version 0.99.7 (2024-04-14)
  • Updating title.

  • Simplifying estimate sparsity description.

               Changes in version 0.99.6 (2024-03-16)

  • Replacing sapply with vapply in simPICsimulate line 238.

               Changes in version 0.99.5 (2024-03-16)
  • Addressing notes after reviewer comments.
  • Updated simPIC count documentation.
  • Updated 1:nCells to seq_len in simPICsimulate line 239.

  • Added documentation for testdata.R.

               Changes in version 0.99.4 (2024-03-10)

  • Fixed issue with system files found that should not be Git tracked in BiocCheck::BiocCheckGitClone

               Changes in version 0.99.3 (2024-03-10)

  • Updating R dependency to R (>=4.4.0)

               Changes in version 0.99.2 (2024-03-09)

  • Fixing issue with system files found in BiocCheck

               Changes in version 0.99.1 (2024-03-09)
  • Addressed reviewer suggestions

  • Major changes include improved docs, including a package man page, text file and code to reproduce test data

               Changes in version 0.99.0 (2024-02-28)
  • Submitted to Bioconductor

SingleCellAlleleExperiment

                   Changes in version 0.99.5

Changes regarding the second round of comments during the Bioconductor submission review:

  • Minor changes to SCAE-show method

  • Extended and moved installation-checks for packages used in optional functionalities to the SCAE-constructor

  • Extended checks for the rowData setter

  • Extended unit tests to increase coverage

                     Changes in version 0.99.4

Changes regarding the first round of comments during the Bioconductor submission review:

Removed multiple dependencies, now listed as suggested

  • computation of the logcounts assay now optional

  • computation of a knee plot and according inflection/knee points now optional

  • computation of new gene-symbols now optional

  • minor changes in tests (needs to be extended to test for new optional code); also extension of the tests to check new code

  • major changes in package structure and organisation

  • reworked vignette to include optional features

                     Changes in version 0.99.3

  • retriggering bioc build during package submission.

                     Changes in version 0.99.2

  • minor changes in the vignette to reduce build-time. Content is the same.

                     Changes in version 0.99.1

  • minor changes made regarding the Bioconductor submission review of scaeData which also affected this package.

                     Changes in version 0.99.0

  • The package is defining a S4 class that is extending the SingleCellExperiment class. The multi-layer data structure integrates data for immune genes at allele and functional level.

  • Workflow: To be able to generate a SingleCellAlleleExperiment object the data has to be generated by the connected workflow single-cell ImmunoGenomic Diversity (scIGD) which performs allele typing and quantification of genes and typed alleles. Use the read_allele_counts() function to read in the data and generate an SCAE object. This function also offers parameters to perform filtering on the data, as well as visualize the filtering step in a so called knee plot.

singleCellTK

             Changes in version 2.12.2 (2024-01-28)

  • Added support for Seurat V5

               Changes in version 2.12.1 (2024-01-10)
  • Updates to documentation
  • Fixes to runTSCAN and plotSeurat Genes
  • Added support for flat file import into SCTK-QC
  • Fixed directory issue in importCellRanger
  • Added Bubble plot to Shiny GUI
  • Updated Dockerfile

sitadela

             Changes in version 1.11.1 (2024-03-07)

NEW FEATURES

  • Updated Ensembl supported versions based on biomaRt

sketchR

                   Changes in version 0.99.2

  • Version bump to trigger new SPB build, no changes

                     Changes in version 0.99.1

  • Version bump to trigger new SPB build, no changes

                     Changes in version 0.99.0

  • Prepare for Bioconductor submission

smartid

                   Changes in version 0.99.5

  • Update scale_mgm() function adding pooled SD option, add details for scale function.

                     Changes in version 0.99.4

  • Add details for TF, IDF, IAE functions.

                     Changes in version 0.99.3

  • Bump R version dependency to >= 4.4 and add details for TF, IDF, IAE functions.

                     Changes in version 0.99.2

  • Added test for gs_score() function.

                     Changes in version 0.99.1

  • Ready for submission to Bioconductor.

                     Changes in version 0.99.0

  • Added a NEWS.md file to track changes to the package.

smoothclust

             Changes in version 0.99.0 (2024-03-17)
  • version for submission to Bioconductor

SNPRelate

                   Changes in version 1.38.0

UTILITIES

  • faster snpgdsLDpruning() and new multi-threading implementation

  • new option ‘autosave’ in snpgdsLDpruning()

  • new option start.pos="random.f500" in snpgdsLDpruning(), allowing faster genotype scanning (it is used by default now). To be compatible with the previous versions, please specify start.pos="random" manually

  • Fix the welcome message when running in a non x86 system

                     Changes in version 1.36.1

UTILITIES

  • fix the compiler warning: -Wformat-security

  • set ‘maf=0.005’ & ‘missing.rate=0.05’ by default in snpgdsLDpruning() (for WGS data)

  • show a progress bar in snpgdsLDpruning() when ‘verbose=TRUE’

  • update the help files of snpgdsAdmixProp() and snpgdsAdmixPlot()

SparseArray

                    Changes in version 1.4.0

NEW FEATURES

  • The following operation are now multithreaded (via OpenMP):
    • SparseMatrix multiplication and crossprod()
    • the matrixStats methods for SparseMatrix objects See ?set_SparseArray_nthread for more information.
  • Define some of the basic coercion methods that used to be defined in the Matrix package but that the lazy Matrix maintainers have decided to deprecate in Matrix 1.7-0 (e.g. coercion from matrix to dgRMatrix).

BUG FIXES

  • Fix aperm(<SVT_SparseArray>) when inner dimensions are not permuted See https://github.com/Bioconductor/SparseArray/issues/6

  • Fix long-standing bug in C function _dotprod_leaf_vector_and_double_col(). In some circumstances the function was reading beyond a C array. Observed effects varied from no observed effects (on Linux) to breaking crossprod() unit tests on arm64 Mac (consistently), on Windows (sporadically), and also probably on PowerPC (or possibly a crash sometimes on this platform. See https://github.com/Bioconductor/SparseArray/issues/2

sparseMatrixStats

                    Changes in version 1.15
  • Throw error if length of ‘center’ in colVars, colSds, colMads (and corrresponding row-functions) does not match size of ‘x’. This behavior was never supported by sparseMatrixStats and previously could return incorrect results. This change matches the upcoming behavior of matrixStats (https://github.com/HenrikBengtsson/matrixStats/issues/254).

SpatialDecon

             Changes in version 1.13.2 (2023-12-28)
  • Compatibility with Seurat v5

SpatialFeatureExperiment

                    Changes in version 1.6.0
  • Changed defaults from sample_id = NULL to sample_id = 1L when dealing with 1 sample or “all” when dealing with multiple samples
  • dim method for BioFormatsImage that doesn’t load the image into memory
  • Deal with univariate spatial results in featureData in cbind and changeSampleID
  • Fixed super embarrassing bug in cbind that fails when combining more than 2 SFE objects
  • Updated readXenium for XOA v2
  • Updated BioFormatsImage to store affine transform info rather than converting to EBImage after transform
  • Speed up affine transformation of sf geometries with sfheaders
  • Coercion from Seurat to SFE
  • SpatRasterImage and EBImage directly inherit from SpatRaster and Image respectively so the user no longer needs to call imgRaster every time they plots or operates on the image, which I find really annoying.
  • Changed name EBImage to ExtImage to reduce confusion
  • Bug fixes on image affine transformation

  • Exporting some util functions: aggBboxes, getPixelSize, and imageIDs

                      Changes in version 1.5.2
  • Added readXenium (for XOA v1)
  • Added BioFormatsImage and EBImage classes to deal with Xenium OME-TIFF
  • Conversion between SpatRasterImage, BioFormatsImage, and EBImage
  • Overhaul of geometry operation functions for images and SFE objects for the new image classes, including bbox, crop, and affine transforms
  • Don’t throw error when there are no rows or columns left after [ subsetting
  • cbind for multiple samples that have rowGeometry

  • Rewrote df2df with the much faster sfheaders, deprecating the less efficient BPPARAM argument

                      Changes in version 1.5.1
  • Added support for rowGeometry and transcript spots
  • Reformat transcript spot files from Vizgen and CosMX
  • Improved readVizgen for transcript spots
  • Added readCosMX

spatialHeatmap

             Changes in version 2.9.6 (2024-04-16)

  • The option of pairwise comparision is added in spatial enrichment.

  • The layout of static network graph is improved.

               Changes in version 2.9.4 (2024-02-10)

  • Added the formal citation.

SpatialOmicsOverlay

                    Changes in version 1.4.0

  • Compatibility with updated labworksheet

  • IPA compatibility

                      Changes in version 1.2.1

  • Corrected labworksheet attached to package

  • Added tibble plottingFactor

  • scale bar printing in mm

  • Bugs fixes:

    • SpatialPosition printing
    • saving xml files
    • ROI matching on string values
    • overcropping on recolored images

Spectra

                    Changes in version 1.13

Changes in 1.13.8

  • Add estimatePrecursorMz() function to estimate the precursor m/z for DDA fragment spectra from previous MS1 spectra issue #315.

Changes in 1.13.7

  • Move generics backendBpparam(), backendParallelFactor() and supportsSetBackend() to ProtGenerics. Required ProtGenerics version 1.35.4 or higher.

Changes in 1.13.6

  • Add filterRanges() and filterValues() functions to allow filtering of a Spectra object based on ranges or similarities of any existing spectraData variables.

Changes in 1.13.5

  • Move generics to ProtGenerics. Requires ProtGenerics version 1.35.3.

Changes in 1.13.4

  • Add entropy and nentropy functions to allow to calculate the (normalized) entropy for each spectrum.

Changes in 1.13.3

  • Fix issue in setBackend that might cause chunk-wise processing to be not run.

Changes in 1.13.2

  • Add possibility to enable and perform chunk-wise (parallel) processing to Spectra: add functions processingChunkSize, backendParallelFactor and processingChunkFactor to set or get definition of chunks for parallel processing. All functions working on peaks data use this mechanism which is implemented in the internal .peaksapply function. The Spectra object gains a new slot “processingChunkSize” that is used to define the size of the processing chunks for the Spectra. See also issue #304. This ensures processing also of very large data sets.

Changes in 1.13.1

  • Fix issue with bin function (see issue #302). Addition of zero.rm parameter to prevent creation of empty bins.

SPIAT

                    Changes in version 1.5.3

BUG FIXES

  • Fixed the wrong layering in plot_cell_categories() and added legend when layer=TRUE

                      Changes in version 1.5.2

NOTES

  • plot_cell_percentages() now returns the plot.

                      Changes in version 1.5.1

BUG FIXES

  • No error message when there are duplicates generated by the “TSNE” option of dimensionality_reduction_plot() function.

  • Deleted duplicated plots returned by plot_cell_categories().

                      Changes in version 1.5.0

Development version on Bioconductor 3.19.

splatter

             Changes in version 1.28.0 (2024-05-01)

  • Properly prevent output from BASiCSEstimate() and scDDSimulate() when verbose = FALSE

  • Minor adjustments to tests to set verbose = FALSE and specify expected warnings

  • Replace the package man page with an auto-generated page

  • Add GitHub usernames and the Bioconductor package URL to description

  • Add @keywords internal and @noRd to function docs where needed

  • Modernise code by restyling using styler and fix other minor issues suggested by BiocCheck

spoon

             Changes in version 0.99.0 (2024-01-18)
  • version for submission to Bioconductor

SpotSweeper

                   Changes in version 0.99.1
  • Added a NEWS.md file to track changes to the package.
  • First full version of the package to be submitted to Bioconductor. See Bioconductor submission here.

SQLDataFrame

                   Changes in version 1.17.1

  • There is a total overhaul of the package implementation. It now defines a 1-dimension DelayedArray called SQLColumnVector to be the basic element which can sit inside a normal DataFrame for delayed operation on-disk. It also defines SQLDataFrame to represent a SQL table (with selected columns), which will be fully file-backed so no data is loaded into memory until requested. This allows uses to represent large datasets in limited memory. SQLDataFrame inherites from DataFrame so it can be used anywhere in Bioconductor’s ecosystem that accepts DataFrame, such as SummarizedExperiment.

  • SQLDataFrame is primarily useful for indicating that the in-memory representation is consistent with the underlying SQL file. It supports all the usual methods for a DataFrame, except that the data is kept on file and referenced as needed. However, only some operations can preserve the SQLDataFrame, such as column subsetting and some cbinding operations. Most operations that add or change data (e.g., filter for row subsetting, mutate for new/modify columns) would collapse to a regular DFrame with SQLColumnVectors before applying the operation. They are still file-backed but lack the guarantee of file consistency. The fallback to DFrame ensures that a SQLDataFrame is interoperable with other Bioconductor data structures that need to perform arbitrary DataFrame operations.

               Changes in version 1.17.0 (2019-10-01)

NEW FEATURES

  • Supports tidy grammar for ‘select’, ‘filter’, ‘mutate’ and ‘%>%’ pipe.

  • Supports representation and saving of MySQL database tables.

  • Supports lazy cross-MySQL database table aggregations, such as join, union, rbind, etc.

BUG FIXES

  • Fixed bugs for single square bracket subsetting with key column(s).

statTarget

                     Changes in version 2.0

NEW FEATURES

  • New GUI o Mouse Hover for help information o .log file

  • New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

  • New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

  • New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

struct

                   Changes in version 1.15.5

  • update automated documentation generation

                     Changes in version 1.15.2

  • add ellipsis to model methods

                     Changes in version 1.15.1

  • remove duplicates when using param_ids for objects with inherited params

  • set check.names = FALSE in DatasetExperiment

SummarizedExperiment

                   Changes in version 1.34.0

NEW FEATURES

  • Add terminators() method, same as promoters() but for terminator regions.

  • Add “Top-level dimnames vs assay-level dimnames” section to vignette. Also fix typo in man/SummarizedExperiment-class.Rd. This is in response to https://github.com/Bioconductor/SummarizedExperiment/issues/79

BUG FIXES

  • Fix typo in man/SummarizedExperiment-class.Rd

SurfR

            Changes in version 0.99.54 (2024-01-14)

  • updated vignette, added references.bib

              Changes in version 0.99.15 (2023-10-09)

  • added README.md file

              Changes in version 0.99.13 (2023-09-26)

  • updated ind_deg.Rd file

              Changes in version 0.99.12 (2023-09-26)

  • removed deprecated rio import

               Changes in version 0.99.7 (2023-09-26)

  • Addressed notes

  • Added BiocFileCache in Gene2SProtein

               Changes in version 0.99.6 (2023-09-25)

  • Addressed notes

               Changes in version 0.99.5 (2023-09-21)

  • Addressed notes

               Changes in version 0.99.4 (2023-09-21)

  • Addressed notes

               Changes in version 0.99.3 (2023-09-11)

  • Removed SurfR.Rproj file and updated gitignore

               Changes in version 0.99.2 (2023-09-11)

  • Removed SurfR.Rproj file and updated gitignore

               Changes in version 0.99.1 (2023-09-11)

  • Updated gitignore

               Changes in version 0.99.0 (2023-08-09)

  • Submitted to Bioconductor

SVMDO

             Changes in version 1.3.0 (2023-12-27)

  • Application of 10-fold cross-validation with tune.svm function from e1071 package

  • Addition of BiocStyle in the Suggestion section of Description file

  • Updating the package citation

  • Updating the package citation

  • Fixing merge-related file section problems occured during the latest pushing process

  • Fixing CITATION-related warning

SynExtend

                   Changes in version 1.15.3

  • Addition of FastLabelOOM function to find communities in graphs/networks on disk space.

                     Changes in version 1.15.2

  • Addition of PrepareSeqs function, beginning the process of deprecating PairSummaries in favor of more cohesive and user friendly functions.

                     Changes in version 1.15.1

  • Fixes bug in JRF distance causing scores to be higher than expected.

TADCompare

             Changes in version 1.13.3 (2024-03-06)

  • Remove rGREAT dependency

               Changes in version 1.13.2 (2024-03-04)

  • Move rGREAT to Imports

               Changes in version 1.13.1 (2024-02-28)

  • Fix build errors

TargetSearch

                    Changes in version 2.6.0

NEW FEATURES

  • New options for ImportFameSettings: New parameter standard can take the RI values. The input file can be also a matrix. Column names can now be specified.

  • A function to plot reference spectra for tsLib objects in a similar style of other visualization tools.

BUG FIXES

  • Check for out-of-bounds in binary search.

DOCUMENTATION

  • Add note of arguments passed to plot via the dots operator. The functions ri_plot_peak and ncdf4_plot_peak accept extra arguments passed to plot and others via the ... argument. However, not all parameters, in particular panel.first and panel.last, will have an effect.

  • Fix misplaced dot man page (RIcorrrect).

  • Fix wrong braces in man page (tsSample-class).

INTERNAL

  • Tidy up NAMESPACE file.

  • Add tests for function ImportFameSettings.

  • Refactor internal code of ImportLibrary and improve the spectrum parser algorithm (allow NA and make sure the format is valid). Add tests cases.

  • Improve tsLib spectrum handling by ensuring the internal data is consistent. Also allow for empty spectra.

  • Improve validity checks for tsProfile and tsMSdata objects. Add tests cases.

                      Changes in version 2.4.2

BUG FIXES

  • Fix maybe-uninitialized warning in some platforms. Set the struct elements to NULL.

  • Fix RI files format incompatibility (affected versions: 2.4.0 and .1). Starting from 2.4.0, these files allow for empty spectra data, but older version raise an error. Therefore, we enforce non empty spectra data to keep compatibility.

                      Changes in version 2.4.1

BUG FIXES

  • An error is thrown if all parameters passed to FindAllPeaks are integers (a rare occurrence). Make sure that arguments are doubles before passing them to the C interface. Also add a test for it.

TCC

                   Changes in version 1.43.4

  • deleted test code related with deprecated functions.

  • deleted ‘baySeq’ dependency codes from vignette and other code.

  • deleted ‘baySeq’ from Depends.

TCGAutils

                   Changes in version 1.24.0

Significant User-visible changes

  • The legacy argument in ID translation functions (UUIDtoBarcode, UUIDtoUUID, barcodeToUUID, and filenameToBarcode) has been defunct and removed.

Bug fixes and minor improvements

  • UUIDtoBarcode ensures that results are ordered based on the input UUIDs.
  • Include informative error message regarding translation of UUIDs from legacy files.

TENxIO

                    Changes in version 1.6.0

Bug fixes and minor improvements

  • Use rowData from filtered SingleCellExperiment object (@MalteThodberg, #5)
  • Add examples to TENxFileList documentation and improve constructor function

tidySpatialExperiment

                   Changes in version 0.99.20

  • tidySpatialExperiment is now in Bioconductor. Documentation has been updated accordingly.

                     Changes in version 0.99.19

  • Improve code style.

                     Changes in version 0.99.18

  • Version bump for Bioconductor.

                     Changes in version 0.99.17

  • Version bump for Bioconductor.

                     Changes in version 0.99.16

  • Version bump for Bioconductor.

                     Changes in version 0.99.15

  • Bug fixes.

                     Changes in version 0.99.14

  • Bug fixes.

                     Changes in version 0.99.13
  • Removed unneeded dependencies.

  • Updated README and vignette material.

                     Changes in version 0.99.12
  • Moved pkgdown website deployment from docs directory to gh-pages branch.

  • Bug fixes.

                     Changes in version 0.99.11

  • Added rworkflow github actions to support continuous and collaborative development.

                     Changes in version 0.99.10

  • Rectangular and elliptical gating added by Quentin Clayssen.

                     Changes in version 0.99.9
  • tidySpatialExperiment now features a NEWS.md file!
  • The package also now has its own pkgdown website.
  • Updated README to better reflect the development of tidyomics ecosystem.

tomoseqr

             Changes in version 1.11.1 (2022-10-25)
  • Made the following changes: o Added 3D visualize function to imageViewer o Changed normCount and normMask options in estimate3dExpressions() to normalize option. When it is TRUE (default), the function works as if normCount = "count", normMask = TRUE. When it is FALSE, the function works as if normCount = "none", normMask = FALSE.

topdownr

                    Changes in version 1.25

Changes in version 1.25.1

  • New version for Bioc 3.19 (devel)
  • Adapt to fragment functions that are moved from MSnbase to PSMatch.

Changes in version 1.19.2

tpSVG

                   Changes in version 0.99.1                        

                   Changes in version 0.99.0

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.

SIGNIFICANT USER-VISIBLE CHANGES

  • Your main changes to a function foo() or parameter param.

BUG FIXES

  • Your bug fixes. See more details at http://bioconductor.org/developers/package-guidelines/#news.

trackViewer

                   Changes in version 1.39.17

  • Fix the legend with alpha for lolliplot.

                     Changes in version 1.39.16

  • Import txdbmaker.

                     Changes in version 1.39.15

  • Optimize the reduce function for loopBouquetPlot.

                     Changes in version 1.39.14

  • reduce the input for loopBouquetPlot.

                     Changes in version 1.39.13

  • Handle the empty input for loopBouquetPlot.

                     Changes in version 1.39.12

  • Update the safe text algorithm for loopBouquetPlot.

                     Changes in version 1.39.11

  • Add parameter safe_text_force for loopBouquetPlot.

                     Changes in version 1.39.10

  • Add color for geneTrack.

                     Changes in version 1.39.9

  • Fix multiple bugs in loopBouquetPlot.

                     Changes in version 1.39.8

  • Change loopBouquetPlot to grid plot.

                     Changes in version 1.39.7

  • Fix the example for loopBouquetPlot.

                     Changes in version 1.39.6

  • add loopBouquetPlot.

                     Changes in version 1.39.5

  • Browse heatmap by js (scratch).

                     Changes in version 1.39.4

  • Fix the issue if the first label is empty for lolliplot.

                     Changes in version 1.39.3

  • Fix the mismatch data track when change the ylim in browseTracks.

                     Changes in version 1.39.2

  • Fix the wrong plot for multiple genes track in browseTracks.

                     Changes in version 1.39.1

  • Fix the y-axis for lollipop plot.

treeclimbR

                   Changes in version 0.99.1
  • Add explicit dependency on R
  • Bug fix - make sure that … are passed on in runDS

  • Internal refactoring to reduce repeated code

                     Changes in version 0.99.0

  • Prepare for Bioconductor submission

                      Changes in version 0.1.5
  • Add NEWS file

treeio

                   Changes in version 1.27.1
  • added support for multiple trees / writing phylo objects in write.beast() (2024-04-08, Mon, #113)
  • speed up read.beast() (2023-12-13, Wed, #118)
  • optimize write.jtree() (2023-12-13, Wed, #117)
  • write.jplace() method to export jplace object to a jplace file (2023-11-27, Mon, #112, #115)

tRNA

             Changes in version 1.21.1 (2024-01-17)
  • replaced deprecated ggplot2 functions

txdbmaker

                    Changes in version 1.0.0
  • The txdbmaker package is a spin-off from the GenomicFeatures package. It includes the following functions, all of them originally from the GenomicFeatures package:
    • browseUCSCtrack
    • getChromInfoFromBiomart
    • makeFDbPackageFromUCSC
    • makeFeatureDbFromUCSC
    • makePackageName
    • makeTxDb
    • makeTxDbFromBiomart
    • makeTxDbFromEnsembl
    • makeTxDbFromGFF
    • makeTxDbFromGRanges
    • makeTxDbFromUCSC
    • makeTxDbPackage
    • makeTxDbPackageFromBiomart
    • makeTxDbPackageFromUCSC
    • supportedMiRBaseBuildValues
    • supportedUCSCFeatureDbTables
    • supportedUCSCFeatureDbTracks
    • supportedUCSCtables
    • UCSCFeatureDbTableSchema

tximeta

                   Changes in version 1.21.4

  • Changing language in docs to “digest” instead of “checksum”.

                     Changes in version 1.21.3
  • GENCODE 44 (H.s.), M34 (M.m), and Ensembl 111
  • RefSeq p13 for human, p6 for mouse

tximport

                   Changes in version 1.31.1
  • Experimental support for oarfish. At this point we are importing number of reads as both ‘abundance’ and ‘counts’.

UCell

                    Changes in version 2.7.6

  • Changed factor for normalization of UCell scores, to account for minimal rank. For typical use cases the behaviour is similar to the previous implementation, but has an impact with very large signatures (UCell score distributions are now more homogeneous). See function UCell:::u_stat()) for details.

                      Changes in version 2.7.4

  • Add support for Seurat v5 assay and datasets in multiple layers. Added dependency on Seurat >= 5.0.

  • Change default for chunk.size to 100. On parallelized jobs, this can improve up to 2-fold execution time.

  • Smaller test dataset (30 cells), to speed up package function checks.

UCSC.utils

                    Changes in version 1.0.0
  • First version of the package that is ready for general use.

UniProt.ws

                   Changes in version 2.44.0

BUG FIXES AND MINOR IMPROVEMENTS

  • No significant changes.

universalmotif

                   Changes in version 1.22.0

BUG FIXES

  • Address C++ compiler warnings.

  • Suppress warnings when using as.data.frame() on DataFrame objects in the SequenceSearches.Rmd vignette.

updateObject

                    Changes in version 1.8.0
  • No changes in this version.

UPDhmm

                   Changes in version 0.99.4

Final corrections and final editing of vignette

                   Changes in version 0.99.3

2nd correction of reviewer’s suggestions

                   Changes in version 0.99.2

Correction of reviewer’s suggestions

                   Changes in version 0.99.1

First pre-review corrections

                   Changes in version 0.99.0

First release of UPDhmm package

variancePartition

                    Changes in version 2.0.5
  • May 31, 2023
  • fix convergence issues
  • fix initialization of lmer() fit

  • use 1 OMP thread internally, then restore to original value

                      Changes in version 2.0.4
  • May 30, 2023
  • When running dream(), ensure model convergence using second fitting with Nelder_Mead to avoid edge cases where the approximate hessian from lmerTest::as_lmerModLT() has a negative eigenvalue
  • fix issue in get_prediction() returning NA values when variables modeled as categorical and levels are omitted
  • fix issue in voomWithDreamWeights() when some genes don’t converge

  • retry lmer() model fit with another optimizer after it fails convergence test.

                      Changes in version 2.0.3
  • May 13, 2023

  • fix vcov()

                      Changes in version 2.0.2
  • May 17, 2023

  • add matrix argument to mvTest()

                      Changes in version 2.0.1
  • May 12, 2023
  • mvTest() now shrinks covariance using the Schafer-Strimmer method

  • vcovSqrt() returns the matrix whose cross product gives the vcov() result from fits with dream()

                      Changes in version 2.0.0
  • April 20, 2023
  • Major code refactoring to:
  • improve code reuse
  • simplify debugging and maintaining code
  • simplify addition of new features
  • improve error handling
  • some linear mixed model analyses are 50% faster

  • enable additional features for dreamlet package that depends heavily on variancePartition.

                     Changes in version 1.33.11
  • Feb 7, 2024
  • fix bug in dream(…,ddf=”Kenward-Roger”) that gave false positives and negatives
  • scaled weights properly to fix this issue, since df in lmerTest::contest() assumes mean of weights is 1.

  • old code used unscaled weights, so df values were too large

                     Changes in version 1.33.10
  • Feb 5, 2024

  • in augmentPriorCount() and voomWithDreamWeights(), add argument scaledByLib=FALSE

                     Changes in version 1.33.9
  • Jan 25, 2024

  • bug fix in BIC() and .fitExtractVarPartModel()

                     Changes in version 1.33.8
  • Jan 22, 2024

  • add BIC() for result of dream() and lmFit()

                     Changes in version 1.33.7
  • Jan 19, 2024

  • add logLik() for result of dream() and lmFit()

                     Changes in version 1.33.6

  • fix issue with subsetting using logicals

                     Changes in version 1.33.5
  • Dec 21, 2023
  • fix issue with ddf always calling “Satterthwaite”
  • enforce subsetting of residuals in assign( “[.MArrayLM2”,)

  • this comes with when rdf < 1

                     Changes in version 1.33.4
  • Dec 13, 2023
  • fix bug with BiocParallel in Windows
  • https://github.com/GabrielHoffman/variancePartition/issues/91

  • handle case where a single contrasts fails in makeContrastsDream()

                     Changes in version 1.33.3
  • Dec 5, 2023

  • in residuals() when dividing by sqrt(1-hatvalues) add small offset to make sure the value is positive

                     Changes in version 1.33.2
  • Nov 13, 2023
  • add augmentPriorCount()

  • add prior.count argument to voomWithDreamWeights() and feed it to augmentPriorCount()

                     Changes in version 1.33.1
  • Nov 2, 2023
  • move omp_set_num_threads() deeper in nesting

velociraptor

                   Changes in version 1.13.1
  • Robust fallback mechanism using basiliskRun option testload=.

VisiumIO

                    Changes in version 1.0.0
  • Package released in Bioconductor!

Voyager

                    Changes in version 1.6.0
  • Option to plot polygon geometry without fill in plotGeometry
  • Option to show axes in both light and dark themes
  • Plot images of classes BioFormatsImage and ExtImage
  • Colorize image plot with different channels
  • Assign different grayscale images to channels
  • Added plotImage to only plot image without plotting geometry

xcms

                     Changes in version 4.1

Changes in version 4.1.13

  • Add parameter rtimeDifferenceThreshold to ObiwarpParam allowing to customize the threshold used by obiwarp to determine whether gaps are present in the sequence of retention times of a sample. This addresses/fixes issue #739.

Changes in version 4.1.12

  • Implementation of the LamaParama class and method for the adjustRtime() function. Allowing alignment of a dataset based on landmarks (lamas) from an external reference dataset.
  • Implementation of related user-level function matchLamasChromPeaks(), summarizeMatchLama() and plot(LamaParama) which allows for evaluation of matching between lamas and chromPeaks.

Changes in version 4.1.11

  • Clean up of required and suggested packages and namespace imports.
  • Re-creation of bundled data objects.

Changes in version 4.1.10

  • Ensure backward compatibility for parameter objects that gained additional slots.

Changes in version 4.1.9

  • Fix bug in filterFeatures,PercentMissingFilter.

Changes in version 4.1.8

  • Fixing issue #716: edit of .empty_chrom_peaks function so an sn column is returned. Fixes extracting and plotting of peaks after using manualChromPeaks

Changes in version 4.1.7

  • Implementation of filterFeatures function with filter parameters: RsdFilter, DratioFilter, PercentMissingFilter, BlankFlag. They can be used ot filter features from XcmsResult and SummarizedExperiment objects.
  • Addition of a section in the main xcms vignette to describe how to use it.

Changes in version 4.1.6

  • Import filterSpectra from MsExperiment.
  • Import breaks_ppm from MsCoreUtils.
  • Update featureArea function to consider all chromatographic peaks per feature, not only the one with the highest intensity. As a consequence, returned m/z and rt ranges might be higher which has an influence in featureChromatograms, EIC-based feature grouping and, to a lesser extent also in gap-filling. Related documentation was updated.
  • Improve performance of the featureArea function (and related of the PeakAreaParam-based gap filling).
  • Add parameter ppm to PeakDensityParam to enable peak-density-based correspondence throgh m/z-dependent bins along the m/z.

Changes in version 4.1.5

  • Improve performance of the chromatogram call for XcmsExperiment objects.
  • Remove internal (not exported) normalization functions. These have been transferred to the MetaboCoreUtils package.
  • Support subsetting of XcmsExperiment with negative indices.

Changes in version 4.1.4

  • Rename variable data in the vignette to faahko.
  • Fix issue in adjustRtime resulting in corrupt processHistory.
  • Add support to perform peakGroups alignment using pre-defined anchor peak matrix (i.e., the numeric matrix with retention times of anchor peaks in the samples that can be used to align these samples).
  • Fix errors related to invalid Chromatogram objects extracted from xcms results: ensure MS level in chromPeaksMatrix is integer.
  • Fix definition of anchor peaks for peakGroups alignment with subset (issue #702).
  • Add filterMsLevel method for MsExperiment and XcmsExperiment.
  • Ensure chunk-wise processing of Spectra (introduced with version 1.13.2) is disabled when xcms is using its own chunk-wise processing.

Changes in version 4.1.3

  • Add parameter verboseBetaColumns to CentWaveParam to enable calculation of additional peak quality metrics comparing the EIC to an idealized bell curve.

Changes in version 4.1.2

  • Add a param = to generic function storeResults: PlainTextParam to save an XcmsExperiment or MsExperiment object as colleciton of plain text files.

Changes in version 4.1.1

  • Add method storeResults and one of its param =: RDataParam to save an XcmsExperiment object as an .RData file.

zellkonverter

                   Changes in version 1.14.0

Major changes

  • Add environment for anndata v0.10.6. This is now the default envrionment for the Python reader/writer.

Minor changes

  • Improve warnings when converting matrices fails

  • Minor change to writing DelayedArray matrices for compatibility with HDF5Array >= v1.31.1

Bug fixes

  • Correctly handle use_backed = TRUE with newer anndata versions

  • Correctly instantiate the anndata v0.10.2 environment

  • Minor fixes for typos etc.

zenith

                    Changes in version 1.5.3
  • March 8, 2024

  • add coef to zenithPR_gsa()

                      Changes in version 1.5.2
  • Feb 2, 2024

  • resolve issue with renameing gene sets when multiple coefs are used

                      Changes in version 1.5.1
  • throw error when zenith is run on multiple coefs

ZygosityPredictor

                    Changes in version 1.3.5

  • fixed small issues in tool and documentation

                      Changes in version 1.3.2

  • Updated tool to revised manuscript

  • New phasing approaches via predefined haploblocks and allelic imbalance

  • Confidence measurement for each gene status

NEWS from existing Data Experiment Packages

CardinalWorkflows

                   Changes in version 1.35.5

SIGNIFICANT USER-VISIBLE CHANGES

  • Add startup message with available vignettes

                     Changes in version 1.35.4

SIGNIFICANT USER-VISIBLE CHANGES

  • Added multiple instance learning to classification vignette

                     Changes in version 1.35.3

BUG FIXES

  • Vignette edits

                     Changes in version 1.35.2

SIGNIFICANT USER-VISIBLE CHANGES

  • Updated vignettes for Cardinal v3.6

                     Changes in version 1.35.1

NEW FEATURES

  • Added ‘exampleMSIData()’ to load data

SIGNIFICANT USER-VISIBLE CHANGES

  • Removed old analysis datasets

curatedPCaData

             Changes in version 0.99.5 (2023-11-02)

  • Bioconductor re-revised version

               Changes in version 0.99.2 (2023-08-10)

  • Bioconductor revised version

               Changes in version 0.99.0 (2023-05-18)

  • Revised whole package according to Bioconductor guidelines

  • Package license is now CC-BY 4.0

CytoMethIC

                   Changes in version 0.99.26

  • Submission of CytoMethIC package.

  • Fixed typos in documentation.

  • Added cmi_checkVersion for user to ensure versions are coordinated

                     Changes in version 0.99.21

  • Submission of CytoMethIC package.

  • Fixed issues mentioned in second review.

DMRcatedata

                   Changes in version 2.20.2

  • EPICv2 data added for vignette

                     Changes in version 2.20.1

  • SNP data added for EPICv2

gDRtestData

          Changes in version 22023-05-15 (2023-05-15)

  • fix related with data.table

             Changes in version 2024-02-28 (2024-02-28)

  • remove redundant annotation files

             Changes in version 2024-02-26 (2024-02-26)

  • improve pkgdown site

  • improved references

  • valid NEWS.md

             Changes in version 2024-02-14 (2024-02-14)

  • make documentation compatible with pkdgdown

             Changes in version 2024-02-07 (2024-02-07)

  • update test data as per new combo model

             Changes in version 2024-02-01 (2024-02-01)

  • standardize full response data functions

             Changes in version 2024-01-30 (2024-01-30)

  • update package vignette

             Changes in version 2024-01-22 (2024-01-22)

  • update testdata

  • add new description fields

             Changes in version 2024-01-04 (2024-01-04)

  • update duplicated functions

             Changes in version 2023-11-22 (2023-11-22)

  • sync master with devel branch

             Changes in version 2023-10-24 (2023-10-24)

  • release Bioc 3.18

  • prerelease Bioc 3.18

             Changes in version 2023-09-18 (2023-09-18)

imcdatasets

             Changes in version 1.11.1 (2024-03-16)
  • Removed defunct functions

JohnsonKinaseData

                   Changes in version 0.99.3

  • Fix selection of left-most central acceptor

  • Add documentation of phospho-peptide processing

                     Changes in version 0.99.2

  • Fix misspelled reference in vignette

                     Changes in version 0.99.1

  • Fix typos

                     Changes in version 0.99.0

  • Initial version

MouseAgingData

                   Changes in version 0.99.13

  • Replaced Parabiosis10x SingleCellExperiment object to include Cell Ontology labels and identifiers

  • Submitted AgingBrain10x_2019NN SingleCellExperiment object for ExperimentHub

                     Changes in version 0.99.0

  • Submitted Parabiosis10x SingleCellExperiment object for ExperimentHub

rRDPData

                   Changes in version 1.23.1

Changes

  • Update data to the RDP Classifier 2.14 released in August 2023 contains the latest bacterial and archaeal taxonomy training set No. 19.

  • The package now contains: 16srrna, fungalits_unite, fungalits_warcup, and fungallsu

scpdata

                   Changes in version 1.11

scpdata 1.11.4

  • fix non-ASCII characters
  • split data.R into multiple data specific files

scpdata 1.11.3

  • leduc2022_pSCoPE: added cellenONE annotations
  • guise2024: added dataset

scpdata 1.11.2

  • khan2023: added dataset.

scpdata 1.11.1

  • Added contribution vignette.
  • gregoire2023_mixCTRL: added dataset.

scRNAseq

                   Changes in version 2.18.0

  • Switched to the ArtifactDB representations for the underlying files. This uses language-agnostic formats (e.g., HDF5, JSON) instead of RDS files to store the various parts of each SingleCellExperiment. The user experience should be more or less the same as the datasets are indistinguishable once loaded into memory.

  • Added the fetchDataset, to create SingleCellExperiment objects from the ArtifactDB file representations. This uses the alabaster.base package to do the loading, with some optional realization of the assays into memory. Advanced users can achieve faster loading times by keeping the assays as file-backed matrices.

  • Introduced saveDataset and related functions to facilitate user uploads of their own datasets. This is accompanied by some step-by-step instructions in the vignette, plus some maintainer instructions in the README.

  • Added searchDatasets to perform text searches on the metadata for each dataset, using the SQLite database compiled from the gypsum backend where the files are stored.

  • Updated some datasets to reflect upstream changes (e.g., in ArrayExpress). Currently, this affects mostly SegerstolpePancreasData, where ArrayExpress decided to change the names and contents of various column annotations.

  • Soft-deprecation of some redundant pieces of information in each dataset. Some examples are the column names of the Zilionis data, which were not unique and had no meaning; or the symbols of the rowData in the Segerstolpe data, which were redundant with the row names. These changes will only take effect when fetchDataset is used directly; the per-dataset getter functions have appropriate back-compatibility patches to restore this information.

  • All getters now have a legacy= option to pull RDS files from ExperimentHub instead of the new formats from gypsum.

seventyGeneData

                   Changes in version 1.39.3

  • Add data-raw directory for data generation scripts.

                     Changes in version 1.39.2

  • Initial modernization of the package.

  • New contributors added.

  • Added a NEWS.md file to track changes to the package.

  • Added a README.md file to describe the package.

  • Update Vignette to use Rmarkdown and BiocStyle.

SFEData

                    Changes in version 1.5.3
  • Added small subset of output files from Vizgen, CosMX, and Xenium to unit test read functions

SingleCellMultiModal

                   Changes in version 1.16.0

New features

  • Added citation information to the package; see citation(“SingleCellMultiModal”) and the vignette.

spatialLIBD

                   Changes in version 1.15.2

SIGNIFICANT USER-VISIBLE CHANGES

  • vis_gene() now has a multi_gene_method argument which provides 3 methods for combining multiple continuous variables: z_score, pca, and sparsity. These options can now be used with run_app() (the interactive websites). These methods are further illustrated and documented in a new vignette available at https://research.libd.org/spatialLIBD/articles/multi_gene_plots.html. This work was contributed by @Nick-Eagles.

SubcellularSpatialData

                   Changes in version 0.99.0
  • Create package

TransOmicsData

                   Changes in version 0.99.5

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.

SIGNIFICANT USER-VISIBLE CHANGES

  • Made changes to vignette to improve usability.

NEWS from existing Workflows

No updated NEWS files.

Deprecated and Defunct Packages

SOFTWARE:

Forty six software packages were removed from this release (after being deprecated in Bioc 3.18):

  • BGmix, bigPint, biodbMirbase, BioMM, Clonality, COHCAP, CSSP, deco, DeepBlueR, DMRforPairs, exomeCopy, fcoex, gaggle, GCSscore, genbankr, GISPA, GOsummaries, GRridge, HPAStainR, imageHTS, IntOMICS, LineagePulse, logitT, LowMACA, LPEadj, macat, mAPKL, mbOmic, Metab, MSstatsSampleSize, multiSight, netbiov, OmicsLonDA, PFP, plethy, pwrEWAS, qrqc, Ringo, SCATE, SEPIRA, seqbias, seqCNA, SISPA, snapCGH, sscore, Travel, trena

  • Please note: baySeq, biomvRCNS, MEIGOR, and RNAdecay, previously announced as deprecated in 3.18, has been updated and remain in Bioconductor. Also previously unannounced packages IntOMICS and COHCAP have been removed without a deprecation cycle.

Seventy software packages are deprecated in this release and will be removed in Bioc 3.20:

  • BDMMAcorrect, beadarraySNP, BHC, biodbLipidmaps, BioNetStat, CancerInSilico, CancerSubtypes, cellHTS2, cliqueMS, CNVgears, compartmap, contiBAIT, CoRegNet, CORREP, CoSIA, crisprseekplus, DNABarcodes, dpeak, EBSeqHMM, eegc, enrichTF, ensemblVEP, exomePeak2, farms, FCBF, flowMap, FoldGO, FScanR, FunChIP, GOSim, HumanTranscriptomeCompendium, ImmuneSpaceR, InterMineR, IntOMICS, IRISFGM, iterClust, maigesPack, metagene, MetaVolcanoR, miRmine, MMAPPR2, MobilityTransformR, multiOmicsViz, NeighborNet, NetPathMiner, oneSENSE, openPrimeRui, pathVar, pcxn, PERFect, phemd, PloGO2, proteasy, PSEA, pwOmics, RefPlus, ReQON, restfulSE, RIPAT, RLSeq, SimBindProfiles, SMAP, sparseDOSSA, SpidermiR, SQUADD, StarBioTrek, STROMA4, TimiRGeN, TNBC.CMS, TnT

EXPERIMENT DATA:

Nine experimental data packages were removed from this release (after being deprecated in BioC 3.18):

  • ccTutorial, ChIC.data, mAPKLData, MAQCsubsetILM, MIGSAdata, pwrEWAS.data, SCATEData, seqCNA.annot, stjudem

  • Please note: DLBCL, previously announced as deprecated in 3.18, has been updated and remain in Bioconductor.

Five experimental data packages are deprecated in this release and will be removed in Bioc 3.20:

  • CoSIAdata, MMAPPR2data, pcxnData, restfulSEData, RLHub

ANNOTATION DATA:

No annotation packages were removed from this release.

One annotation package is deprecated in this release and will be removed in Bioc 3.20.

  • MafH5.gnomAD.v3.1.2.GRCh38

WORKFLOWS:

No workflow packages were removed from this release.

No workflow packages were deprecated in this release.

BOOKS:

No books were removed from this release.

No books were deprecated in this release.