| 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, COSMIC ,Wormbase and Gramene) |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| Category | Biocore Team c/o BioC user list | Category Analysis |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| clusterProfiler | Guangchuang Yu | statistical analysis and visulization of functional profiles for genes and gene clusters |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| ecolitk | Laurent Gautier | Meta-data and tools for E. coli |
| ENVISIONQuery | Alex Lisovich , Roger Day | Retrieval from the ENVISION bioinformatics data portal into R |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gaggle | Christopher Bare | Broadcast data between R and Gaggle |
| 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) |
| genomes | Chris Stubben | Genome sequencing project metadata |
| GenomicFeatures | Biocore Team c/o BioC user list | Tools for making and manipulating transcript centric annotations |
| GenomicRanges | Biocore Team c/o BioC user list | Representation and manipulation of genomic intervals |
| GlobalAncova | Manuela Hummel | 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 |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| GOstats | Biocore Team c/o BioC user list | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| joda | Ewa Szczurek | JODA algorithm for quantifying gene deregulation using knowledge |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Biocore Team c/o BioC user list | Client-side SOAP access KEGG |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| 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 |
| R453Plus1Toolbox | Hans-Ulrich Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| RBioinf | Robert Gentleman | RBioinf |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| RMAPPER | Heike Sichtig , Alberto Riva | R interface to the MAPPER database of transcription factor binding sites |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| 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 |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |