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

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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.

Author
Wolfgang Kaisers
Date of publication
2016-05-14 00:08:41
Maintainer
Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
License
GPL-2
Version
1.7.0

View on CRAN

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...

Files in this package

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