| Package | Maintainer | Title |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| edd | Vince Carey | expression density diagnostics |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing Association of Groups of Genes with a Clinical Variable |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| siggenes | Holger Schwender | SAM and Efron's empirical Bayes approaches |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
