| 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 |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| HTqPCR | Heidi Dvinge , Paul Bertone | Automated analysis of qPCR data |
| 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 |
| 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. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| 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 |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |