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.

AuthorWolfgang Kaisers
Date of publication2016-05-14 00:08:41
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseGPL-2
Version1.7.0

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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

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