| Package | Maintainer | Title |
|---|---|---|
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| ADaCGH2 | Ramon Diaz-Uriarte | Analysis of data from aCGH experiments using parallel computing and ff objects |
| 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 |
| 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 |
| 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 |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| 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. |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| 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. |
| chopsticks | Hin-Tak Leung | The snp.matrix and X.snp.matrix classes |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| Clonality | Irina Ostrovnaya | Clonality testing |
| cn.farms | Andreas Mitterecker , Djork-Arne Clevert | cn.farms - Factor Analysis for copy number estimation |
| 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 |
| CoGAPS | Elana J. Fertig , Michael F. Ochs | Coordinated Gene Activity in Pattern Sets |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| coRNAi | Elin Axelsson | Analysis of co-knock-down RNAi data |
| 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 |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| 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 |
| EBarrays | Ming Yuan | Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification |
| 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 |
| ExiMiR | Sylvain Gubian | R functions for the normalization of Exiqon miRNA array data |
| 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 |
| 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 |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowPlots | N. Hawkins | flowPlots: analysis plots and data class for gated flow cytometry data |
| flowQ | F. Hahne | Quality 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 |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gaia | S. Morganella | GAIA: An R package for genomic analysis of significant chromosomal aberrations. |
| GeneGA | Zhenpeng Li | Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm |
| 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 genetics of gene expression (c) 2006 VJ Carey |
| GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
| GlobalAncova | Manuela Hummel | 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 |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| 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 | Automated analysis of high-throughput qPCR data |
| HTSanalyzeR | Xin Wang | Gene set over-representation, enrichment and network analyses for high-throughput screens |
| imageHTS | Gregoire Pau | Analysis of high-throughput microscopy-based screens |
| IsoGeneGUI | Setia Pramana | A graphical user interface to conduct a dose-response analysis of microarray 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 |
| les | Julian Gehring | Identifying Differential Effects 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 |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| 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 |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| 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 |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| MotIV | Eloi Mercier , Raphael Gottardo | Motif Identification and Validation |
| Mulcom | Claudio Isella | Calculates MulCom test |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| 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 | Preprocessing tools for 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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| phenoDist | Xian Zhang | Phenotypic distance measures |
| phenoTest | Evarist Planet | Tools to test correlation between gene expression and phenotype. |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| pint | Olli-Pekka Huovilainen | Pairwise INTegration of functional genomics data |
| 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 |
| 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 |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| RBioinf | Robert Gentleman | RBioinf |
| reb | Karl J. Dykema | Regional Expression Biases |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| rGADEM | Arnaud Droit | de novo motif discovery |
| 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 |
| RNAinteract | Bernd Fischer | Estimate Pairwise Interactions from multidimensional features |
| 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 |
| 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. |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| 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. |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| snpAssoc | David Clayton | Enhanced SnpMatrix and XSnpMatrix classes |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| snpMatrix | David Clayton | The snp.matrix and X.snp.matrix classes |
| snpStats | David Clayton | SnpMatrix and XSnpMatrix classes and methods |
| 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 |
| survcomp | Benjamin Haibe-Kains , Markus Schroeder | Performance Assessment and Comparison for Survival Analysis |
| tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| TurboNorm | Maarten van Iterson | A fast scatterplot smoother suitable for microarray normalization |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| Vega | Sandro Morganella | An R package for copy number data segmentation |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| 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 |