refGenome: Gene and Splice Site Annotation Using Annotation Data from Ensembl and UCSC Genome Browsers
Version 1.7.3

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.

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

Getting started

Package overview

Popular man pages

addIsCoding: Add information on coding/non-coding status.
ensemblGenome-class: Class '"ensemblGenome"'
extractByGeneName: Extract subsets of refGenome by gene-name.
getGenePositions: Extract subsets of refGenome by gene-name.
overlapJuncs: overlapJuncs function
readGtf: Reading and parsing GTF files into refGenome objects.
refExons-class: Class '"refExons"'
See all...

All man pages Function index File listing

Man pages

addIsCoding: Add information on coding/non-coding status.
ensemblGenome-class: Class '"ensemblGenome"'
extractByGeneID: Extract subsets of refGenome by gene-ID.
extractByGeneName: Extract subsets of refGenome by gene-name.
geneList-class: Class '"geneList"'
geneModel-class: Class '"geneModel"'
getGeneId: Extract gene ID from gene-name and getGeneId.
getGenePositions: Extract subsets of refGenome by gene-name.
overlap: overlap function
overlapJuncs: overlapJuncs function
readGtf: Reading and parsing GTF files into refGenome objects.
refExons-class: Class '"refExons"'
refGenome-class: Class '"refGenome"'
refGenome-package: Managing annotation data for reference Genomes from UCSC and...
refJunctions-class: Class '"refJunctions"'
saveGenome: Saving and loading 'refGenome' objects
transcriptModel-class: Class '"transcriptModel"'
ucscGenome-class: Class '"ucscGenome"'
unifyJuncs: Unification of splice-junctions.
unifyRanges: Unification of Exonic ranges.
writeDB: Saving and loading 'refGenome' objects to and from SQLite...

Functions

+,geneList,geneList-method Man page
+,geneModel,geneModel-method Man page
[,geneList,ANY,ANY,ANY-method Man page
addEnsembl Man page
addEnsembl,ucscGenome-method Man page
addEnsembl-methods Man page
addIsCoding Man page
addIsCoding,ensemblJunctions-method Man page
addIsCoding-methods Man page
addIsoforms Man page
addIsoforms,ucscGenome-method Man page
addIsoforms-methods Man page
addXref Man page
addXref,ucscGenome-method Man page
addXref-methods Man page
basedir Man page
basedir,refGenome-method Man page
basedir-methods Man page
basedir<- Man page
basedir<-,refGenome-method Man page
basedir<--methods Man page
ensPrimAssembly Man page Source code
ensemblExons Man page Source code
ensemblExons-class Man page
ensemblGenome Man page Source code
ensemblGenome-class Man page
ensemblJunctions Man page Source code
ensemblJunctions-class Man page
extractByGeneId Man page
extractByGeneId,refGenome,character-method Man page
extractByGeneId,refJunctions,character-method Man page
extractByGeneId-methods Man page
extractByGeneName Man page
extractByGeneName,refGenome,character-method Man page
extractByGeneName,refJunctions,character-method Man page
extractByGeneName-methods Man page
extractFeature Man page
extractFeature,refGenome,character-method Man page
extractFeature-methods Man page
extractPaGenes Man page
extractPaGenes,ensemblGenome-method Man page
extractPaGenes-methods Man page
extractSeqids Man page
extractSeqids,refGenome-method Man page
extractSeqids-methods Man page
extractTranscript Man page
extractTranscript,refGenome,character-method Man page
extractTranscript,ucscGenome-method Man page
extractTranscript-methods 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,ensemblGenome,character-method Man page
geneList,ensemblGenome,factor-method Man page
geneList,ucscGenome,character-method Man page
geneList,ucscGenome,factor-method Man page
geneList-class Man page
geneList-methods Man page
geneModel Man page
geneModel,ensemblGenome,character-method Man page
geneModel,ucscGenome,character-method Man page
geneModel-class Man page
geneModel-methods 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,transcriptModel-method Man page
getCdsData-methods Man page
getExonData Man page
getExonData,transcriptModel-method Man page
getExonData-methods 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,refJunctions,ANY-method Man page
getGenePositions,ucscGenome,ANY-method Man page
getGenePositions,ucscGenome-method Man page
getGenePositions-methods Man page
getGeneTable Man page
getGeneTable,ensemblGenome-method Man page
getGeneTable,ucscGenome-method Man page
getGeneTable-methods Man page
getGtf Man page
getGtf,refGenome-method Man page
getGtf-methods Man page
getSpliceTable Man page
getSpliceTable,refGenome-method Man page
getSpliceTable-methods Man page
getTranscript Man page
getTranscript,geneModel,character-method Man page
getTranscript,geneModel,numeric-method Man page
getTranscript-methods Man page
getTranscriptFromGtf Source code
getXref Man page
getXref,ucscGenome-method Man page
getXref-methods 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 Source code
loadGenomeDb Man page Source code
names,geneList-method Man page
names<-,geneList,character-method Man page
names<-,geneList,numeric-method Man page
onUnload Source code
overlap Man page Source code
overlapJuncs Man page Source code
overlap_seqs Source code
plot.geneModel Man page Source code
plot.transcriptModel Man page Source code
plotUbs Man page
plotUbs,unifiedExons-method Man page
plotUbs-methods Man page
read.gtf Man page
read.gtf,refGenome-method Man page
read.gtf-methods Man page
refExons Man page
refExons,refGenome-method Man page
refExons-class Man page
refExons-methods Man page
refGenome-class Man page
refGenome-package Man page
refJunctions Man page
refJunctions-class Man page
saveGenome Man page
saveGenome,refGenome-method Man page
saveGenome-methods Man page
setGtf Man page
setGtf,refGenome-method Man page
setGtf-methods Man page
show,geneList-method Man page
tableFeatures Man page
tableFeatures,ensemblGenome-method Man page
tableFeatures,ucscGenome-method Man page
tableFeatures-methods Man page
tableSeqids Man page
tableSeqids,refGenome-method Man page
tableSeqids-methods Man page
tableTranscript.id Man page
tableTranscript.id,ensemblGenome-method Man page
tableTranscript.id,ucscGenome-method Man page
tableTranscript.id-methods Man page
tableTranscript.name Man page
tableTranscript.name,ensemblGenome-method Man page
tableTranscript.name-methods Man page
transcriptModel-class Man page
ucPrimAssembly Man page Source code
ucscExons Man page Source code
ucscExons-class Man page
ucscGenome Man page Source code
ucscGenome-class Man page
ucscJunctions Man page Source code
ucscJunctions-class Man page
uid Source code
unifiedExons-class Man page
unifyJuncs Man page
unifyJuncs,refJunctions-method Man page
unifyJuncs-methods Man page
unifyRanges Man page
unifyRanges,refExons-method Man page
unifyRanges-methods Man page
writeDB Man page
writeDB,refGenome-method Man page
writeDB-methods 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
refGenome documentation built on May 19, 2017, 8:53 p.m.

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