refGenome: Gene and Splice Site Annotation Using Annotation Data from Ensembl and UCSC Genome Browsers

Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.

Install the latest version of this package by entering the following in R:
install.packages("refGenome")
AuthorWolfgang Kaisers
Date of publication2017-03-20 09:03:07 UTC
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseGPL-2
Version1.7.3

View on CRAN

Functions

addEnsembl Man page
addEnsembl-methods Man page
addEnsembl,ucscGenome-method Man page
addIsCoding Man page
addIsCoding,ensemblJunctions-method Man page
addIsCoding-methods Man page
addIsoforms Man page
addIsoforms-methods Man page
addIsoforms,ucscGenome-method Man page
addXref Man page
addXref-methods Man page
addXref,ucscGenome-method Man page
basedir Man page
basedir<- Man page
basedir<--methods Man page
basedir-methods Man page
basedir<-,refGenome-method Man page
basedir,refGenome-method Man page
ensemblExons Man page
ensemblExons-class Man page
ensemblGenome Man page
ensemblGenome-class Man page
ensemblJunctions Man page
ensemblJunctions-class Man page
ensPrimAssembly Man page
extractByGeneId Man page
extractByGeneId-methods Man page
extractByGeneId,refGenome,character-method Man page
extractByGeneId,refJunctions,character-method Man page
extractByGeneName Man page
extractByGeneName-methods Man page
extractByGeneName,refGenome,character-method Man page
extractByGeneName,refJunctions,character-method Man page
extractFeature Man page
extractFeature-methods Man page
extractFeature,refGenome,character-method Man page
extractPaGenes Man page
extractPaGenes,ensemblGenome-method Man page
extractPaGenes-methods Man page
extractSeqids Man page
extractSeqids-methods Man page
extractSeqids,refGenome-method Man page
extractTranscript Man page
extractTranscript-methods Man page
extractTranscript,refGenome,character-method Man page
extractTranscript,ucscGenome-method Man page
geneId<- Man page
geneId<-,geneModel,character-method Man page
geneId<-,geneModel,factor-method Man page
geneId<--methods Man page
geneList Man page
[,geneList,ANY,ANY,ANY-method Man page
geneList-class Man page
geneList,ensemblGenome,character-method Man page
geneList,ensemblGenome,factor-method Man page
+,geneList,geneList-method Man page
geneList-methods Man page
geneList,ucscGenome,character-method Man page
geneList,ucscGenome,factor-method Man page
geneModel Man page
geneModel-class Man page
geneModel,ensemblGenome,character-method Man page
+,geneModel,geneModel-method Man page
geneModel-methods Man page
geneModel,ucscGenome,character-method Man page
geneName<- Man page
geneName<-,geneModel,character-method Man page
geneName<-,geneModel,factor-method Man page
geneName<--methods Man page
getCdsData Man page
getCdsData-methods Man page
getCdsData,transcriptModel-method Man page
getExonData Man page
getExonData-methods Man page
getExonData,transcriptModel-method Man page
getGeneId Man page
getGeneId,ensemblGenome,character-method Man page
getGeneId,ensemblGenome,factor-method Man page
getGeneId-methods Man page
getGenePositions Man page
getGenePositions,ensemblGenome,character-method Man page
getGenePositions,ensemblGenome,missing-method Man page
getGenePositions-methods Man page
getGenePositions,refJunctions,ANY-method Man page
getGenePositions,ucscGenome,ANY-method Man page
getGenePositions,ucscGenome-method Man page
getGeneTable Man page
getGeneTable,ensemblGenome-method Man page
getGeneTable-methods Man page
getGeneTable,ucscGenome-method Man page
getGtf Man page
getGtf-methods Man page
getGtf,refGenome-method Man page
getSpliceTable Man page
getSpliceTable-methods Man page
getSpliceTable,refGenome-method Man page
getTranscript Man page
getTranscript,geneModel,character-method Man page
getTranscript,geneModel,numeric-method Man page
getTranscript-methods Man page
getXref Man page
getXref-methods Man page
getXref,ucscGenome-method Man page
initialize,geneList-method Man page
initialize,geneModel-method Man page
initialize,refGenome-method Man page
initialize,transcriptModel-method Man page
length,geneList-method Man page
loadGenome Man page
loadGenomeDb Man page
names<-,geneList,character-method Man page
names,geneList-method Man page
names<-,geneList,numeric-method Man page
overlap Man page
overlapJuncs Man page
plot.geneModel Man page
plot.transcriptModel Man page
plotUbs Man page
plotUbs-methods Man page
plotUbs,unifiedExons-method Man page
read.gtf Man page
read.gtf-methods Man page
read.gtf,refGenome-method Man page
refExons Man page
refExons-class Man page
refExons-methods Man page
refExons,refGenome-method Man page
refGenome-class Man page
refGenome-package Man page
refJunctions Man page
refJunctions-class Man page
saveGenome Man page
saveGenome-methods Man page
saveGenome,refGenome-method Man page
setGtf Man page
setGtf-methods Man page
setGtf,refGenome-method Man page
show,geneList-method Man page
tableFeatures Man page
tableFeatures,ensemblGenome-method Man page
tableFeatures-methods Man page
tableFeatures,ucscGenome-method Man page
tableSeqids Man page
tableSeqids-methods Man page
tableSeqids,refGenome-method Man page
tableTranscript.id Man page
tableTranscript.id,ensemblGenome-method Man page
tableTranscript.id-methods Man page
tableTranscript.id,ucscGenome-method Man page
tableTranscript.name Man page
tableTranscript.name,ensemblGenome-method Man page
tableTranscript.name-methods Man page
transcriptModel-class Man page
ucPrimAssembly Man page
ucscExons Man page
ucscExons-class Man page
ucscGenome Man page
ucscGenome-class Man page
ucscJunctions Man page
ucscJunctions-class Man page
unifiedExons-class Man page
unifyJuncs Man page
unifyJuncs-methods Man page
unifyJuncs,refJunctions-method Man page
unifyRanges Man page
unifyRanges-methods Man page
unifyRanges,refExons-method Man page
writeDB Man page
writeDB-methods Man page
writeDB,refGenome-method Man page

Files

inst
inst/extdata
inst/extdata/hs.ensembl.62.small.RData
inst/extdata/hs.ucsc.small.RData
inst/extdata/hs.ensembl.76.small.gtf
inst/extdata/hs.ensembl.62.small.gtf
inst/extdata/hs_en82_grch38_small.gtf
inst/doc
inst/doc/refGenome.Rnw
inst/doc/readGTF.Rnw
inst/doc/readGTF.pdf
inst/doc/refGenome.pdf
inst/doc/refGenome.R inst/doc/readGTF.R
tests
tests/test-all.R
src
src/Makevars
src/grange.h
src/gtf.h
src/refGenome.cpp
src/refGenome.h
src/data_frame.h
src/Makevars.win
src/extptr.h
src/tokenize.h
NAMESPACE
NEWS
R
R/geneModel.R R/refGenome.R
vignettes
vignettes/refGenome.Rnw
vignettes/readGTF.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/refGenome-package.Rd man/refJunctions-class.Rd man/addIsCoding.Rd man/writeDB.Rd man/overlap.Rd man/getGenePositions.Rd man/ensemblGenome-class.Rd man/refGenome-class.Rd man/unifyJuncs.Rd man/transcriptModel-class.Rd man/ucscGenome-class.Rd man/unifyRanges.Rd man/extractByGeneName.Rd man/geneList-class.Rd man/refExons-class.Rd man/extractByGeneID.Rd man/saveGenome.Rd man/readGtf.Rd man/geneModel-class.Rd man/getGeneId.Rd man/overlapJuncs.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.