Bioconductor Task View: Annotation

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Package Maintainer Title
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips.
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 Annotation for microarrays
biomaRt Steffen Durinck Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot)
Category S. Falcon Category Analysis
ChromoViz Jihoon Kim Multimodal visualization of gene expression data
DynDoc Biocore Team Dynamic document tools
ecolitk Laurent Meta-data and tools for E. coli
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 S. Falcon Tools for manipulating GO and microarrays.
goTools Agnes Paquet Functions for Gene Ontology database
KEGGSOAP J. Zhang Client-side SOAP access KEGG
matchprobes Biocore Team Tools for sequence matching of probes on arrays
nem Florian Markowetz Nested Effects Models to reconstruct phenotypic hierarchies
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
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data