| Package | Maintainer | Title |
|---|---|---|
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count data |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| CGEN | William Wheeler | An R package for analysis of case-control studies in genetic epidemiology |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| GOstats | Biocore Team c/o BioC user list | Tools for manipulating GO and microarrays. |
| 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 |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| Mulcom | Claudio Isella | Calculates MulCom test |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| 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 |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| phenoTest | Evarist Planet | Tools to test correlation between gene expression and phenotype. |
| PROMISE | Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| segmentSeq | Thomas J. Hardcastle | Methods for identifying small RNA loci from high-throughput sequencing data |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |