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.
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
altcdfenvs Laurent Gautier alternative CDF environments (aka mappings)
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.
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
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
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 Association of Groups of Genes with a Clinical Variable
goProfiles Alex Sanchez goProfiles: an R package for the statistical analysis of functional profiles
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 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 Florian Markowetz Nested Effects Models to reconstruct phenotypic hierarchies
occugene Oliver Will Functions for Multinomial Occupancy Distribution
pdInfoBuilder Benilton Carvalho Platform Design Information Package Builder
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
RSNPper VJ Carey interface to for SNP-related data
rtracklayer Michael Lawrence R interface to genome browsers and their annotation tracks
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
xmapbridge Tim Yates Export plotting files to the xmapBridge for visualisation in X:Map