| Package | Maintainer | Title |
|---|---|---|
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization 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 |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| 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 |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| betr | Martin Aryee | Identify differentially expressed genes in microarray time-course data |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| CGHbase | Sjoerd Vosse | CGHbase: Base functions and classes for arrayCGH data analysis. |
| CGHregions | Mark van de Wiel | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| CNVtools | Chris Barnes | A package to test genetic association with CNV data |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| 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. |
| 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 |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| edd | Vince Carey | expression density diagnostics |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array 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 |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowQ | F. Hahne | Qualitiy control for flow cytometry |
| flowStats | Florian Hahne and Chao-Jen Wong | Statistical methods for the analysis of flow cytometry data |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| 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 |
| GGBase | Vince Carey | infrastructure for genetics of gene expression (c) 2008 VJ Carey |
| GGtools | Vince Carey | software and data for genetical genomics (c) 2006 VJ Carey |
| 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 |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| HTqPCR | Heidi Dvinge , Paul Bertone | Automated analysis of qPCR data |
| ITALICS | Guillem Rigaill | ITALICS |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| LMGene | John Tillinghast | LMGene Software for Date 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 |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| 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 |
| 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 |
| methylumi | Sean Davis | Handle Illumina methylation data |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oligo | Benilton Carvalho | Tools for low-level analysis of oligonucleotide arrays. |
| 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. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| 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) |
| 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. |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| puma | Richard Pearson | 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 |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| reb | Karl J. Dykema | Regional Expression Biases |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| 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 |
| 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. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| 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 |
| splicegear | Laurent Gautier | splicegear |
| 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 |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |