| Package | Maintainer | Title |
|---|---|---|
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DESeq | Simon Anders | Digital gene expresion analysis based on the negative binomial distribution |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| 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. |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |