annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("annmap")
AuthorTim Yates <Tim.Yates@cruk.manchester.ac.uk>
Bioconductor views Annotation Microarray OneChannel ReportWriting Transcription Visualization
Date of publicationNone
MaintainerChris Wirth <Christopher.Wirth@cruk.manchester.ac.uk>
LicenseGPL-2
Version1.18.0
http://annmap.cruk.manchester.ac.uk

View on Bioconductor

Functions

allArrays Man page
allChromosomes Man page
allDomains Man page
allEstExons Man page
allEstGenes Man page
allEstTranscripts Man page
allExons Man page
allGenes Man page
allPredictionTranscripts Man page
allProbes Man page
allProbesets Man page
allProteins Man page
allSymbols Man page
allSynonyms Man page
allTranscripts Man page
annmap Man page
annmapAddConnection Man page
annmapAll Man page
annmapClearCache Man page
annmapConnect Man page
annmapDetails Man page
annmapDisconnect Man page
annmapEnv Man page
annmapFilters Man page
annmapGenePlot Man page
annmapGetParam Man page
annmap-package Man page
annmapRange Man page
annmapRangeApply Man page
annmapSeqname Man page
annmapSetParam Man page
annmapTo Man page
annmapToggleCaching Man page
annmapUtils Man page
arrayDetails Man page
arrayToProbeset Man page
arrayType Man page
chromosomeDetails Man page
codingProbesets Man page
convertBamToRle Man page
domainDetails Man page
domainInRange Man page
domainInRange,character-method Man page
domainInRange,data.frame-method Man page
domainInRange,factor-method Man page
domainInRange,GRanges-method Man page
domainInRange,NULL-method Man page
domainInRange,RangedData-method Man page
domainToGene Man page
domainToProbeset Man page
domainToProtein Man page
domainToTranscript Man page
estExonDetails Man page
estExonInRange Man page
estExonInRange,character-method Man page
estExonInRange,data.frame-method Man page
estExonInRange,factor-method Man page
estExonInRange,GRanges-method Man page
estExonInRange,NULL-method Man page
estExonInRange,RangedData-method Man page
estExonToEstGene Man page
estExonToEstTranscript Man page
estExonToProbeset Man page
estGeneDetails Man page
estGeneInRange Man page
estGeneInRange,character-method Man page
estGeneInRange,data.frame-method Man page
estGeneInRange,factor-method Man page
estGeneInRange,GRanges-method Man page
estGeneInRange,NULL-method Man page
estGeneInRange,RangedData-method Man page
estGeneToEstExon Man page
estGeneToEstTranscript Man page
estGeneToProbeset Man page
estTranscriptDetails Man page
estTranscriptInRange Man page
estTranscriptInRange,character-method Man page
estTranscriptInRange,data.frame-method Man page
estTranscriptInRange,factor-method Man page
estTranscriptInRange,GRanges-method Man page
estTranscriptInRange,NULL-method Man page
estTranscriptInRange,RangedData-method Man page
estTranscriptToEstExon Man page
estTranscriptToEstGene Man page
estTranscriptToProbeset Man page
exonDetails Man page
exonic Man page
exonInRange Man page
exonInRange,character-method Man page
exonInRange,data.frame-method Man page
exonInRange,factor-method Man page
exonInRange,GRanges-method Man page
exonInRange,NULL-method Man page
exonInRange,RangedData-method Man page
exonToGene Man page
exonToProbeset Man page
exonToTranscript Man page
geneDetails Man page
geneInRange Man page
geneInRange,character-method Man page
geneInRange,data.frame-method Man page
geneInRange,factor-method Man page
geneInRange,GRanges-method Man page
geneInRange,NULL-method Man page
geneInRange,RangedData-method Man page
generalisedNameToEnsembl Man page
generalisedNameToNCBI Man page
generateBridgeData Man page
geneToDomain Man page
geneToExon Man page
geneToExonProbeset Man page
geneToExonProbesetExpr Man page
geneToGeneRegionTrack Man page
geneToProbeset Man page
geneToProtein Man page
geneToSymbol Man page
geneToSynonym Man page
geneToTranscript Man page
genomeToProteinCoords Man page
genomeToTranscriptCoords Man page
genomicExonDepthPlot Man page
genomicPlot Man page
genomicProbePlot Man page
hasProbes Man page
hasProbesAtleast Man page
hasProbesBetween Man page
hasProbesIn Man page
intergenic Man page
intronic Man page
isExonic Man page
isIntergenic Man page
isIntronic Man page
isUnreliable Man page
ngsBridgePlot Man page
ngsTraceLabel Man page
ngsTracePlotter Man page
ngsTraceScale Man page
nonIntronicGeneLength Man page
nonIntronicTranscriptLength Man page
predictionTranscriptDetails Man page
predictionTranscriptInRange Man page
predictionTranscriptInRange,character-method Man page
predictionTranscriptInRange,data.frame-method Man page
predictionTranscriptInRange,factor-method Man page
predictionTranscriptInRange,GRanges-method Man page
predictionTranscriptInRange,NULL-method Man page
predictionTranscriptInRange,RangedData-method Man page
predictionTranscriptToPredictionExon Man page
predictionTranscriptToProbeset Man page
probeDetails Man page
probeInRange Man page
probeInRange,character-method Man page
probeInRange,data.frame-method Man page
probeInRange,factor-method Man page
probeInRange,GRanges-method Man page
probeInRange,NULL-method Man page
probeInRange,RangedData-method Man page
probesetDetails Man page
probesetInRange Man page
probesetInRange,character-method Man page
probesetInRange,data.frame-method Man page
probesetInRange,factor-method Man page
probesetInRange,GRanges-method Man page
probesetInRange,NULL-method Man page
probesetInRange,RangedData-method Man page
probesetToCdnatranscript Man page
probesetToDomain Man page
probesetToEstExon Man page
probesetToEstGene Man page
probesetToEstTranscript Man page
probesetToExon Man page
probesetToGene Man page
probesetToHit Man page
probesetToPredictionTranscript Man page
probesetToProbe Man page
probesetToProtein Man page
probesetToTranscript Man page
probeToHit Man page
probeToProbeset Man page
proteinCoordsToGenome Man page
proteinDetails Man page
proteinInRange Man page
proteinInRange,character-method Man page
proteinInRange,data.frame-method Man page
proteinInRange,factor-method Man page
proteinInRange,GRanges-method Man page
proteinInRange,NULL-method Man page
proteinInRange,RangedData-method Man page
proteinToDomain Man page
proteinToGene Man page
proteinToProbeset Man page
proteinToTranscript Man page
seqnameMapping Man page
seqnamesToEnsembl Man page
seqnamesToNCBI Man page
spliceGroupIndex Man page
spliceIndex Man page
strandAsInteger Man page
symbolToEstGene Man page
symbolToEstTranscript Man page
symbolToGene Man page
symbolToTranscript Man page
synonymDetails Man page
synonymToEstGene Man page
synonymToEstTranscript Man page
synonymToGene Man page
synonymToTranscript Man page
transcriptCoordsToGenome Man page
transcriptDetails Man page
transcriptInRange Man page
transcriptInRange,character-method Man page
transcriptInRange,data.frame-method Man page
transcriptInRange,factor-method Man page
transcriptInRange,GRanges-method Man page
transcriptInRange,NULL-method Man page
transcriptInRange,RangedData-method Man page
transcriptToCdnaprobeset Man page
transcriptToCodingExon Man page
transcriptToCodingRange Man page
transcriptToDomain Man page
transcriptToExon Man page
transcriptToExonProbeset Man page
transcriptToGene Man page
transcriptToProbeset Man page
transcriptToProtein Man page
transcriptToSynonym Man page
transcriptToTranslatedprobes Man page
transcriptToUtrExon Man page
transcriptToUtrRange Man page
unreliable Man page
utrProbesets Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/cache.R R/coords.R R/db.R R/filtering.R R/plot.genomic.R R/plot.ngs.R R/si.R R/statements.R R/utils.R R/utr.R R/ws.R R/zzz.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/README
inst/cookbook
inst/cookbook/Sweave.sty
inst/cookbook/cookbook.Rnw
inst/cookbook/delia.R
inst/cookbook/yellow-exclamation.png
inst/databases.txt
inst/doc
inst/doc/INSTALL.Rnw
inst/doc/INSTALL.pdf
inst/doc/annmap.Rnw
inst/doc/annmap.pdf
inst/doc/cookbook.Rnw
inst/doc/cookbook.pdf
inst/ngsGridPlotExample.R
inst/rdata
inst/rdata/HG-U133Plus2.tp53.expr.RData
inst/rdata/HuEx-1_0.tp53.expr.RData
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/commaConfig
inst/unitTests/commaConfig/databases.txt
inst/unitTests/runit.TEMPLATE.R inst/unitTests/runit.all-statements.R inst/unitTests/runit.cache.R inst/unitTests/runit.coords.R inst/unitTests/runit.data.R inst/unitTests/runit.db.R inst/unitTests/runit.detail-statements.R inst/unitTests/runit.extras.R inst/unitTests/runit.plots.R inst/unitTests/runit.range-statements.R inst/unitTests/runit.to-statements.R inst/unitTests/runit.utils.R inst/unitTests/runit.utr.R inst/unitTests/runit.ws.R
inst/unitTests/tabConfig
inst/unitTests/tabConfig/databases.txt
man
man/annmap-package.Rd man/annmap.all.Rd man/annmap.coords.Rd man/annmap.details.Rd man/annmap.env.Rd man/annmap.filters.Rd man/annmap.range.Rd man/annmap.seqname.Rd man/annmap.spliceIndex.Rd man/annmap.to.Rd man/annmap.utils.Rd man/annmap.utr.Rd man/plot.genomic.Rd man/plot.ngs.Rd
tests
tests/doRUnit.R
vignettes
vignettes/INSTALL.Rnw
vignettes/Makefile
vignettes/annmap.Rnw
vignettes/cookbook.Rnw

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