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
read.gtf                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 Ensembl.
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 databases.
