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.
|Date of publication||2016-05-14 00:08:41|
|Maintainer||Wolfgang Kaisers <email@example.com>|
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...