| 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 CDF environments (aka probeset mappings) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| 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. |
| arrayQualityMetrics | Audrey Kauffmann | Quality metrics on microarray data sets |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene) |
| Category | Robert Gentleman | Category Analysis |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| 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 | Dan Tenenbaum | Broadcast data between R and other bioinformatics programs |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| GeneRfold | Antoine Lucas | R for genes and sequences, using viennaRNA package (fold) |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| goProfiles | Alex Sanchez | goProfiles: an R package for the statistical analysis of functional profiles |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorth | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Robert Gentleman | Client-side SOAP access KEGG |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| matchprobes | Biocore Team c/o BioC user list | Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
| PAnnBuilder | Li Hong | Protein annotation data package builder |
| pdInfoBuilder | Benilton Carvalho | Platform Design Information Package Builder |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| rtracklayer | Michael Lawrence | R interface to genome browsers and their annotation tracks |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| xmapbridge | Tim Yates | Export plotting files to the xmapBridge for visualisation in X:Map |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |