| Package | Maintainer | Title |
|---|---|---|
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| ExiMiR | Sylvain Gubian | R functions for the normalization of Exiqon miRNA array data |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| les | Julian Gehring | Identifying Differential Effects in Tiling Microarray Data |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| splicegear | Laurent Gautier | splicegear |
| tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |