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 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