| Package | Maintainer | Title |
|---|---|---|
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| altcdfenvs | Laurent Gautier | alternative cdfenvs |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| AnnBuilder | J. Zhang | Bioconductor annotation data package builder |
| annotate | Biocore Team c/o BioC user list | Annotation for microarrays |
| AnnotationDbi | Biocore Team c/o BioC user list | Annotation Database Interface |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot) |
| Category | Robert Gentleman | Category Analysis |
| ChromoViz | Jihoon Kim | Multimodal visualization of gene expression data |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| ecolitk | Laurent | Meta-data and tools for E. coli |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| gaggle | Paul Shannon | Broadcast data between R and Java bioinformatics programs |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| 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 |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| KEGGSOAP | Robert Gentleman | Client-side SOAP access KEGG |
| matchprobes | Biocore Team c/o BioC user list | Tools for sequence matching of probes on arrays |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| pdInfoBuilder | Vince Carey | Platform Design Information Package Builder |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| RMAPPER | VJ Carey | interface to mapper.chip.org |
| RSNPper | VJ Carey | interface to chip.org::SNPper for SNP-related data |
| SemSim | Xiang Guo | Gene Ontology-based Semantic Similarity Measures |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |