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refGenome (version 1.7.7)

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

Description

Contains functionalities for importing and managing 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.

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Version

Install

install.packages('refGenome')

Monthly Downloads

138

Version

1.7.7

License

GPL-2

Maintainer

Wolfgang Kaisers

Last Published

May 22nd, 2019

Functions in refGenome (1.7.7)

overlapJuncs

overlapJuncs function
geneModel-class

Class "geneModel"
ucscGenome-class

Class "ucscGenome"
ensemblGenome-class

Class "ensemblGenome"
unifyRanges

Unification of Exonic ranges.
writeDB

Saving and loading refGenome objects to and from SQLite databases.
addIsCoding

Add information on coding/non-coding status.
unifyJuncs

Unification of splice-junctions.
saveGenome

Saving and loading refGenome objects
refJunctions-class

Class "refJunctions"
read.gtf

Reading and parsing GTF files into refGenome objects.
refExons-class

Class "refExons"
extractByGeneId

Extract subsets of refGenome by gene-ID.
overlap

overlap function
getGeneId

Extract gene ID from gene-name and getGeneId.
extractByGeneName

Extract subsets of refGenome by gene-name.
geneList-class

Class "geneList"
getGenePositions

Extract subsets of refGenome by gene-name.
transcriptModel-class

Class "transcriptModel"
refGenome-class

Class "refGenome"
refGenome-package

Managing annotation data for reference Genomes from UCSC and Ensembl.