| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| ADaCGH2 | Ramon Diaz-Uriarte | Analysis of data from aCGH experiments using parallel computing and ff objects |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| AffyCompatible | Martin Morgan | Affymetrix GeneChip software compatibility |
| affyContam | V. Carey | structured corruption of affymetrix cel file data |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affyILM | Myriam Kroll and Fabrice Berger | Linear Model of background subtraction and the Langmuir isotherm |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affyPara | Markus Schmidberger | Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays |
| affypdnn | Laurent Gautier | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| affyQCReport | Craig Parman | QC Report Generation for affyBatch objects |
| AffyTiling | Charles G. Danko | Easy extraction of individual probes in Affymetrix tiling arrays |
| Agi4x44PreProcess | Pedro Lopez-Romero | PreProcessing of Agilent 4x44 array data |
| AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| annotate | Biocore Team c/o BioC user list | Annotation for microarrays |
| AnnotationDbi | Biocore Team c/o BioC user list | Annotation Database Interface |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| ArrayExpress | Audrey Kauffmann | Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
| arrayMvout | V. Carey | multivariate outlier detection for expression array QA |
| arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
| arrayQualityMetrics | Audrey Kauffmann | Quality metrics on microarray data sets |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| attract | Jessica Mar | Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| BayesPeak | Jonathan Cairns | Bayesian Analysis of ChIP-seq Data |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count data |
| BCRANK | Adam Ameur | Predicting binding site consensus from ranked DNA sequences |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadDataPackR | Mike Smith | Compression of Illumina BeadArray data |
| betr | Martin Aryee | Identify differentially expressed genes in microarray time-course data |
| bgafun | Iain Wallace | BGAfun A method to identify specifity determining residues in protein families |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| BHC | Rich Savage | Bayesian Hierarchical Clustering |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| Biobase | Biocore Team c/o BioC user list | Biobase: Base functions for Bioconductor |
| BiocCaseStudies | Biocore Team c/o BioC user list | BiocCaseStudies: Support for the Case Studies Monograph |
| biocDatasets | L. Gautier | Synthetic datasets for bioconductor |
| biocGraph | Florian Hahne | Graph examples and use cases in Bioinformatics |
| biocViews | Biocore Team c/o BioC user list | Categorized views of R package repositories |
| bioDist | Biocore Team c/o BioC user list | Different distance measures |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene) |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| BioSeqClass | Li Hong | Classification for Biological Sequences |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| BufferedMatrix | Benjamin Milo Bolstad | A matrix data storage object held in temporary files |
| BufferedMatrixMethods | B. M. Bolstad | Microarray Data related methods that utlize BufferedMatrix objects |
| BUS | Yuanhua Liu | Gene network reconstruction |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| CAMERA | Carsten Kuhl | Collection of annotation related methods for mass spectrometry data |
| Category | Biocore Team c/o BioC user list | Category Analysis |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| CGEN | William Wheeler | An R package for analysis of case-control studies in genetic epidemiology |
| CGHbase | Sjoerd Vosse | CGHbase: Base functions and classes for arrayCGH data analysis. |
| CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
| CGHregions | Sjoerd Vosse | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| charm | Martin Aryee | Analysis of DNA methylation data from CHARM microarrays |
| ChemmineR | ChemmineR Team | Analysis of Small Molecule and Screening Data |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| chipseq | Biocore Team c/o BioC user list | chipseq: A package for analyzing chipseq data |
| ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| ChromHeatMap | Tim F. Rayner | Heat map plotting by genome coordinate |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
| CMA | Christoph Bernau | Synthesis of microarray-based classification |
| CNTools | J. Zhang | Convert segment data into a region by sample matrix to allow for other high level computational analyses. |
| CNVtools | Chris Barnes | A package to test genetic association with CNV data |
| CoCiteStats | Biocore Team c/o BioC user list | Different test statistics based on co-citation. |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| CoGAPS | Elana J. Fertig , Michael F. Ochs | Coordinated Gene Activity in Pattern Sets |
| ConsensusClusterPlus | Matt Wilkerson | ConsensusClusterPlus |
| convert | Yee Hwa (Jean) Yang | Convert Microarray Data Objects |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| coRNAi | Elin Axelsson | Analysis of co-knock-down RNAi data |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| cosmo | Oliver Bembom | Supervised detection of conserved motifs in DNA sequences |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| CRImage | Henrik Failmezger , Yinyin Yuan | CRImage a package to classify cells and calculate tumour cellularity |
| crlmm | Benilton S Carvalho , Robert Scharpf , Matt Ritchie | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| cycle | Matthias Futschik | Significance of periodic expression pattern in time-series data |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DAVIDQuery | Roger Day | Retrieval from the DAVID bioinformatics data resource into R |
| ddCt | Jitao David Zhang | The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DEGraph | Laurent Jacob | Two-sample tests on a graph |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DESeq | Simon Anders | Digital gene expresion analysis based on the negative binomial distribution |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| dualKS | Eric J. Kort | Dual KS Discriminant Analysis and Classification |
| dyebias | Philip Lijnzaad | The GASSCO method for correcting for slide-dependent gene-specific dye bias |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| EBarrays | Ming Yuan | Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification |
| EBImage | Gregoire Pau | Image processing toolbox for R |
| ecolitk | Laurent Gautier | Meta-data and tools for E. coli |
| edd | Vince Carey | expression density diagnostics |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| eisa | Gabor Csardi | Expression data analysis via the Iterative Signature Algorithm |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| ExpressionView | Gabor Csardi | Visualize biclusters identified in gene expression data |
| externalVector | Biocore Team c/o BioC user list | Vector objects for R with external storage |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| farms | Djork-Arne Clevert | FARMS - Factor Analysis for Robust Microarray Summarization |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flagme | Mark Robinson | Analysis of Metabolomics GC/MS Data |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFlowJo | John J. Gosink | Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm. |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowMeans | Nima Aghaeepour | Non-parametric Flow Cytometry Data Gating |
| flowMerge | Greg Finak | Cluster Merging for Flow Cytometry Data |
| flowQ | F. Hahne | Qualitiy control for flow cytometry |
| flowStats | Florian Hahne and Chao-Jen Wong | Statistical methods for the analysis of flow cytometry data |
| flowTrans | Greg Finak | Parameter Optimization for Flow Cytometry Data Transformation |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| frma | Matthew N. McCall | Frozen RMA and Barcode |
| frmaTools | Matthew N. McCall | Frozen RMA Tools |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gaggle | Dan Tenenbaum | Broadcast data between R and other bioinformatics programs |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| GeneAnswers | Gang Feng and Pan Du | Integrated Interpretation of Genes |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| GeneGA | Zhenpeng Li | Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm |
| GeneMeta | Biocore Team c/o BioC user list | MetaAnalysis for High Throughput Experiments |
| geneplotter | Biocore Team c/o BioC user list | Graphics related functions for Bioconductor |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GeneRfold | Antoine Lucas | R for genes and sequences, using viennaRNA package (fold) |
| GeneSelectMMD | Weiliang Qiu | Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions |
| GeneSelector | Martin Slawski | Stability and Aggregation of ranked gene lists |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneticsDesign | The R Genetics Project | Functions for designing genetics studies |
| GeneticsPed | David Henderson | Pedigree and genetic relationship functions |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| genoCN | Wei Sun | genotyping and copy number study tools |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| genomeIntervals | Julien Gagneur | Operations on genomic intervals |
| genomes | Chris Stubben | Genome sequencing project metadata |
| GenomicFeatures | Biocore Team c/o BioC user list | Tools for making and manipulating transcript centric annotations |
| GenomicRanges | Biocore Team c/o BioC user list | Representation and manipulation of genomic intervals |
| Genominator | James Bullard | Analyze, manage and store genomic data |
| GEOmetadb | Jack Zhu | A compilation of metadata from NCBI GEO |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| GEOsubmission | Alexandre Kuhn | Prepares microarray data for submission to GEO |
| GGBase | Vince Carey | infrastructure for genetics of gene expression (c) 2008 VJ Carey |
| GGtools | Vince Carey | software and data for genetics of gene expression (c) 2006 VJ Carey |
| girafe | J. Toedling | Genome Intervals and Read Alignments for Functional Exploration |
| GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| goProfiles | Alex Sanchez | goProfiles: an R package for the statistical analysis of functional profiles |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| GOstats | Biocore Team c/o BioC user list | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| graph | Seth Falcon | graph: A package to handle graph data structures |
| GraphAlignment | Joern P. Meier | GraphAlignment |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| GSEABase | Biocore Team c/o BioC user list | Gene set enrichment data structures and methods |
| GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hexbin | Nicholas Lewin-Koh | Hexagonal Binning Routines |
| HilbertVis | Simon Anders | Hilbert curve visualization |
| HilbertVisGUI | Simon Anders | HilbertVisGUI |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| HTSanalyzeR | Xin Wang | Gene set over-representation, enrichment and network analyses for high-throughput screens |
| hyperdraw | Paul Murrell | Visualizing Hypergaphs |
| hypergraph | Biocore Team c/o BioC user list | A package providing hypergraph data structures |
| Icens | Biocore Team c/o BioC user list | NPMLE for Censored and Truncated Data |
| iChip | Qianxing Mo | Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models |
| idiogram | Karl J. Dykema | idiogram |
| imageHTS | Gregoire Pau | Analysis of high-throughput microscopy-based screens |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| IRanges | Biocore Team c/o BioC user list | Infrastructure for manipulating intervals on sequences |
| iSeq | Qianxing Mo | Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models |
| IsoGeneGUI | Setia Pramana | A graphical user interface to conduct a dose-response analysis of microarray data |
| ITALICS | Guillem Rigaill | ITALICS |
| iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
| iterativeBMAsurv | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Biocore Team c/o BioC user list | Client-side SOAP access KEGG |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| les | Julian Gehring | Identifying Loci of Enhanced Significance in Tiling Microarray Data |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| LMGene | Blythe Durbin-Johnson | LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| logitT | Tobias Guennel | logit-t Package |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| LPEadj | Carl Murie | A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| LVSmiRNA | Stefano Calza | LVS normalization for Agilent miRNA data |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| MassSpecWavelet | Pan Du | Mass spectrum processing by wavelet-based algorithms |
| MBCB | Jeff Allen | MBCB (Model-based Background Correction for Beadarray) |
| mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| MCRestimate | Marc Johannes | Misclassification error estimation with cross-validation |
| mdqc | Gabriela Cohen-Freue | Mahalanobis Distance Quality Control for microarrays |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| MEDME | Mattia Pelizzola | Modelling Experimental Data from MeDIP Enrichment |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| metahdep | John R. Stevens | Hierarchical Dependence in Meta-Analysis |
| methVisual | Arie Zackay | Methods for visualization and statistics on DNA methylation data |
| methylumi | Sean Davis | Handle Illumina methylation data |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MiChip | Jonathon Blake | MiChip Parsing and Summarizing Functions |
| microRNA | Chao-Jen Wong | Data and functions for dealing with microRNAs |
| minet | Patrick E. Meyer | Mutual Information NETworks |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| MotIV | Eloi Mercier , Raphael Gottardo | Motif Identification and Validation |
| Mulcom | Claudio Isella | Calculates MulCom test |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| NTW | Yuanhua Liu | Predict gene network using an Ordinary Differential Equation (ODE) based method |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| NuPoP | Ji-Ping Wang | An R package for nucleosome positioning prediction |
| occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| oligoClasses | Benilton Carvalho and Robert Scharpf | Classes for high-throughput arrays supported by oligo |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| oneChannelGUI | Raffaele A Calogero | This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. Next Generation Sequencing secondary analysis for ncRNA quantification is also available. |
| ontoCAT | Natalja Kurbatova | Ontology parsing |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| OTUbase | Daniel Beck | Deals with OTU data |
| OutlierD | Sukwoo Kim | Outlier detection using quantile regression on the M-A scatterplots of high-throughput data |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| PAnnBuilder | Li Hong | Protein annotation data package builder |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| pathRender | Li Long | Render molecular pathways |
| PatientGeneSets | Simina M. Boca | Patient-oriented gene-set analysis |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| PCpheno | Nolwenn Le Meur | Phenotypes and cellular organizational units |
| pdInfoBuilder | Benilton Carvalho | Platform Design Information Package Builder |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| PGSEA | Karl Dykema | Parametric Gene Set Enrichment Analysis |
| pgUtils | Johannes Rainer | Utility functions for PostgreSQL databases |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| pint | Olli-Pekka Huovilainen | Pairwise INTegration of functional genomics data |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| plateCore | Errol Strain | Statistical tools and data structures for plate-based flow cytometry |
| plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| PLPE | Soo-heang Eo | Local Pooled Error Test for Differential Expression with Paired High-throughput Data |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| preprocessCore | Benjamin Milo Bolstad | A collection of pre-processing functions |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| PROMISE | Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
| puma | Richard Pearson , Li Zhang | Propagating Uncertainty in Microarray Analysis |
| qpcrNorm | Jessica Mar | Data-driven normalization strategies for high-throughput qPCR data. |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| R453Plus1Toolbox | H-U Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| RbcBook1 | Vince Carey | Support for Springer monograph on Bioconductor |
| RBGL | Li Long | An interface to the BOOST graph library |
| RBioinf | Robert Gentleman | RBioinf |
| rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
| RCytoscape | Paul Shannon | Display and manipulate graphs in Cytoscape |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| Rdisop | Steffen Neumann | Decomposition of Isotopic Patterns |
| RDRToolbox | Christoph Bartenhagen | A package for nonlinear dimension reduction with Isomap and LLE. |
| reb | Karl J. Dykema | Regional Expression Biases |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| rGADEM | Arnaud Droit | de novo motif discovery |
| Rgraphviz | Kasper Hansen | Provides plotting capabilities for R graph objects |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
| RMAPPER | Heike Sichtig , Alberto Riva | R interface to the MAPPER database of transcription factor binding sites |
| rMAT | Arnaud Droit and Raphael Gottardo | R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. |
| RmiR | Francesco Favero | Package to work with miRNAs and miRNA targets with R |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| RpsiXML | Jitao David Zhang | R interface to PSI-MI 2.5 files |
| Rredland | VJ Carey | interface to redland RDF utilities |
| Rsamtools | Biocore Team c/o BioC user list | Import aligned BAM file format sequences into R / Bioconductor |
| rsbml | Michael Lawrence | R support for SBML, using libsbml |
| RTCA | Jitao David Zhang | Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| rtracklayer | Michael Lawrence | R interface to genome browsers and their annotation tracks |
| Rtreemix | Jasmina Bogojeska | Rtreemix: Mutagenetic trees mixture models. |
| Ruuid | Biocore Team c/o BioC user list | Ruuid: Provides Universally Unique ID values |
| RWebServices | Martin Morgan | Expose R functions as web services through Java/Axis/Apache |
| sagenhaft | Tim Beissbarth | Collection of functions for reading and comparing SAGE libraries |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| SamSPECTRAL | Habil Zare | Identifies cell population in flow cytometry data. |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| segmentSeq | Thomas J. Hardcastle | Methods for identifying small RNA loci from high-throughput sequencing data |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| ShortRead | Biocore Team c/o BioC user list | Classes and methods for high-throughput short-read sequencing data. |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| SIM | Maarten van Iterson | Integrated Analysis on two human genomic datasets |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SJava | Martin Morgan | The Omegahat interface for R and Java. |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| SMAP | Robin Andersson | A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| snpMatrix | David Clayton | The snp.matrix and X.snp.matrix classes |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| spkTools | Matthew N McCall | Methods for Spike-in Arrays |
| splicegear | Laurent Gautier | splicegear |
| splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| SQUADD | Martial Sankar | Add-on of the SQUAD Software |
| SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| SSPA | Maarten van Iterson | Sample Size and Power Analysis for Microarray Data |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| TargetSearch | Alvaro Cuadros-Inostroza | A package for the analysis of GC-MS metabolite profiling data. |
| tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| tkWidgets | J. Zhang | R based tk widgets |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| tspair | Jeffrey T. Leek | Top Scoring Pairs for Microarray Classification |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| weaver | Seth Falcon | Tools and extensions for processing Sweave documents |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
| xcms | Colin A. Smith | LC/MS and GC/MS Data Analysis |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| xmapbridge | Tim Yates | Export plotting files to the xmapBridge for visualisation in X:Map |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |