| Package | Maintainer | Title |
|---|---|---|
| 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 |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count data |
| 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 |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| 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 |
| 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 |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| 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 |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| 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 |
| 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 |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| 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 |
| IsoGeneGUI | Setia Pramana | A graphical user interface to conduct a dose-response analysis of microarray data |
| 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 |
| LMGene | Blythe Durbin-Johnson | LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| 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 |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| metahdep | John R. Stevens | Hierarchical Dependence in Meta-Analysis |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| 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 |
| 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 |
| 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. |
| puma | Richard Pearson , Li Zhang | Propagating Uncertainty in Microarray Analysis |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| 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 |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| survcomp | Benjamin Haibe-Kains , Markus Schroeder | Performance Assessment and Comparison for Survival Analysis |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| 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 |