| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| affyContam | V. Carey | structured corruption of affymetrix cel file data |
| 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 |
| 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) |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| 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 |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| 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 |
| 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 |
| 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 |
| bioDist | Biocore Team c/o BioC user list | Different distance measures |
| BioSeqClass | Li Hong | Classification for Biological Sequences |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| BUS | Yuanhua Liu | Gene network reconstruction |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| Category | Robert Gentleman | Category Analysis |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
| CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
| charm | Martin Aryee | Analysis of DNA methylation data from CHARM microarrays |
| ChemmineR | Y. Eddie Cao | A Compound Data Mining Framework |
| chipseq | Biocore Team c/o BioC user list | chipseq: A package for analyzing chipseq data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| 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 |
| CoCiteStats | R. Gentleman | Different test statistics based on co-citation. |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| ConsensusClusterPlus | Matt Wilkerson | ConsensusClusterPlus |
| 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 |
| 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. |
| 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 |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression 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-depedent gene-specific dye bias |
| 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) |
| ExpressionView | Gabor Csardi | Visualize biclusters identified in gene expression data |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| 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 |
| 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 |
| 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 |
| 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 |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| gene2pathway | Marc Johannes | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team c/o BioC user list | MetaAnalysis for High Throughput Experiments |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneSelectMMD | Weiliang Qiu | Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions |
| 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 |
| 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 |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| 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 |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| 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 |
| iFlow | Kyongryun Lee | GUI based visualization for flow cytometry |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| 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 |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| 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 |
| 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 Microarrays |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| 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 |
| mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| MCRestimate | Marc Johannes | Misclassification error estimation with cross-validation |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| 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 |
| 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 |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| 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. |
| 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. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| 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 |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| 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 |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
| 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 |
| 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 |
| 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. |
| Rtreemix | Jasmina Bogojeska | Rtreemix: Mutagenetic trees mixture models. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| SamSPECTRAL | Habil Zare | Identifies cell population in flow cytometry data. |
| segmentSeq | Thomas J. Hardcastle | Takes high-throughput sequencing data and uses it to define segments of the genome to which a high density of reads align. |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| ShortRead | Biocore Team c/o BioC user list | Base 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 |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| 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 |
| 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 |
| 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 |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| 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 |