| Package | Maintainer | Title |
|---|---|---|
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| EBarrays | Deepayan Sarkar | Empirical Bayes for Microarrays |
| edd | Vince Carey | expression density diagnostics |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| 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 |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | Geun Cheol Lee | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| maanova | Lei Wu | Tools for analyzing Micro Array experiments |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differeneces in Time Course Microarray Data |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| pcot2 | Sarah Song | Principle Coordinates and Hotelling's T-Square method |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| plgem | Mattia Pelizzola | Power Law Global Error Model |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| siggenes | Holger Schwender | SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarry Sample Size |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| webbioc | Colin A. Smith | Bioconductor Web Interface |