A B E G I L N O P R S T U W misc
refGenome-package | Managing annotation data for reference Genomes from UCSC and Ensembl. |
addEnsembl | Class '"ucscGenome"' |
addEnsembl-method | Class '"ucscGenome"' |
addEnsembl-methods | Class '"ucscGenome"' |
addIsCoding | Add information on coding/non-coding status. |
addIsCoding-method | Add information on coding/non-coding status. |
addIsCoding-methods | Add information on coding/non-coding status. |
addIsoforms | Class '"ucscGenome"' |
addIsoforms-method | Class '"ucscGenome"' |
addIsoforms-methods | Class '"ucscGenome"' |
addXref | Class '"ucscGenome"' |
addXref-method | Class '"ucscGenome"' |
addXref-methods | Class '"ucscGenome"' |
basedir | Class '"refGenome"' |
basedir-method | Class '"refGenome"' |
basedir-methods | Class '"refGenome"' |
basedir<- | Class '"refGenome"' |
basedir<--method | Class '"refGenome"' |
basedir<--methods | Class '"refGenome"' |
ensemblExons | Class '"refExons"' |
ensemblExons-class | Class '"refExons"' |
ensemblGenome | Class '"ensemblGenome"' |
ensemblGenome-class | Class '"ensemblGenome"' |
ensemblJunctions | Class '"refJunctions"' |
ensemblJunctions-class | Class '"refJunctions"' |
ensPrimAssembly | Class '"refGenome"' |
extractByGeneId | Extract subsets of refGenome by gene-ID. |
extractByGeneId-method | Extract subsets of refGenome by gene-ID. |
extractByGeneId-methods | Extract subsets of refGenome by gene-ID. |
extractByGeneName | Extract subsets of refGenome by gene-name. |
extractByGeneName-method | Extract subsets of refGenome by gene-name. |
extractByGeneName-methods | Extract subsets of refGenome by gene-name. |
extractFeature | Class '"refGenome"' |
extractFeature-method | Class '"refGenome"' |
extractFeature-methods | Class '"refGenome"' |
extractPaGenes | Class '"ensemblGenome"' |
extractPaGenes-method | Class '"ensemblGenome"' |
extractPaGenes-methods | Class '"ensemblGenome"' |
extractSeqids | Class '"refGenome"' |
extractSeqids-method | Class '"refGenome"' |
extractSeqids-methods | Class '"refGenome"' |
extractTranscript | Class '"refGenome"' |
extractTranscript-method | Class '"refGenome"' |
extractTranscript-method | Class '"ucscGenome"' |
extractTranscript-methods | Class '"refGenome"' |
geneId<- | Class '"geneModel"' |
geneId<--method | Class '"geneModel"' |
geneId<--methods | Class '"geneModel"' |
geneList | Class '"geneList"' |
geneList-class | Class '"geneList"' |
geneList-method | Class '"geneList"' |
geneList-methods | Class '"geneList"' |
geneModel | Class '"geneModel"' |
geneModel-class | Class '"geneModel"' |
geneModel-method | Class '"geneModel"' |
geneModel-methods | Class '"geneModel"' |
geneName<- | Class '"geneModel"' |
geneName<--method | Class '"geneModel"' |
geneName<--methods | Class '"geneModel"' |
getCdsData | Class '"transcriptModel"' |
getCdsData-method | Class '"transcriptModel"' |
getCdsData-methods | Class '"transcriptModel"' |
getExonData | Class '"transcriptModel"' |
getExonData-method | Class '"transcriptModel"' |
getExonData-methods | Class '"transcriptModel"' |
getGeneId | Extract gene ID from gene-name and getGeneId. |
getGeneId-method | Extract gene ID from gene-name and getGeneId. |
getGeneId-methods | Extract gene ID from gene-name and getGeneId. |
getGenePositions | Extract subsets of refGenome by gene-name. |
getGenePositions-method | Extract subsets of refGenome by gene-name. |
getGenePositions-method | Class '"ucscGenome"' |
getGenePositions-methods | Extract subsets of refGenome by gene-name. |
getGeneTable | Class '"ensemblGenome"' |
getGeneTable-method | Class '"ensemblGenome"' |
getGeneTable-method | Class '"ucscGenome"' |
getGeneTable-methods | Class '"ensemblGenome"' |
getGtf | Class '"refGenome"' |
getGtf-method | Class '"refGenome"' |
getGtf-methods | Class '"refGenome"' |
getSpliceTable | Class '"refJunctions"' |
getSpliceTable-method | Class '"refJunctions"' |
getSpliceTable-methods | Class '"refJunctions"' |
getTranscript | Class '"transcriptModel"' |
getTranscript-method | Class '"transcriptModel"' |
getTranscript-methods | Class '"transcriptModel"' |
getXref | Class '"ucscGenome"' |
getXref-method | Class '"ucscGenome"' |
getXref-methods | Class '"ucscGenome"' |
initialize-method | Class '"geneList"' |
initialize-method | Class '"geneModel"' |
initialize-method | Class '"refGenome"' |
initialize-method | Class '"transcriptModel"' |
length-method | Class '"geneList"' |
loadGenome | Saving and loading 'refGenome' objects |
loadGenomeDb | Saving and loading 'refGenome' objects to and from SQLite databases. |
names-method | Class '"geneList"' |
names<--method | Class '"geneList"' |
overlap | overlap function |
overlapJuncs | overlapJuncs function |
plot.geneModel | Class '"geneModel"' |
plot.transcriptModel | Class '"transcriptModel"' |
plotUbs | Unification of Exonic ranges. |
plotUbs-method | Unification of Exonic ranges. |
plotUbs-methods | Unification of Exonic ranges. |
read.gtf | Reading and parsing GTF files into refGenome objects. |
read.gtf-method | Reading and parsing GTF files into refGenome objects. |
read.gtf-methods | Reading and parsing GTF files into refGenome objects. |
refExons | Class '"refExons"' |
refExons-class | Class '"refExons"' |
refExons-method | Class '"refExons"' |
refExons-methods | Class '"refExons"' |
refGenome-class | Class '"refGenome"' |
refJunctions | Class '"refJunctions"' |
refJunctions-class | Class '"refJunctions"' |
saveGenome | Saving and loading 'refGenome' objects |
saveGenome-method | Saving and loading 'refGenome' objects |
saveGenome-methods | Saving and loading 'refGenome' objects |
setGtf | Class '"refGenome"' |
setGtf-method | Class '"refGenome"' |
setGtf-methods | Class '"refGenome"' |
show-method | Class '"geneList"' |
tableFeatures | Class '"ensemblGenome"' |
tableFeatures-method | Class '"ensemblGenome"' |
tableFeatures-method | Class '"ucscGenome"' |
tableFeatures-methods | Class '"ensemblGenome"' |
tableSeqids | Class '"refGenome"' |
tableSeqids-method | Class '"refGenome"' |
tableSeqids-methods | Class '"refGenome"' |
tableTranscript.id | Class '"ensemblGenome"' |
tableTranscript.id-method | Class '"ensemblGenome"' |
tableTranscript.id-method | Class '"ucscGenome"' |
tableTranscript.id-methods | Class '"ensemblGenome"' |
tableTranscript.name | Class '"ensemblGenome"' |
tableTranscript.name-method | Class '"ensemblGenome"' |
tableTranscript.name-methods | Class '"ensemblGenome"' |
transcriptModel-class | Class '"transcriptModel"' |
ucPrimAssembly | Class '"refGenome"' |
ucscExons | Class '"refExons"' |
ucscExons-class | Class '"refExons"' |
ucscGenome | Class '"ucscGenome"' |
ucscGenome-class | Class '"ucscGenome"' |
ucscJunctions | Class '"refJunctions"' |
ucscJunctions-class | Class '"refJunctions"' |
unifiedExons-class | Class '"refExons"' |
unifyJuncs | Unification of splice-junctions. |
unifyJuncs-method | Unification of splice-junctions. |
unifyJuncs-methods | Unification of splice-junctions. |
unifyRanges | Unification of Exonic ranges. |
unifyRanges-method | Unification of Exonic ranges. |
unifyRanges-methods | Unification of Exonic ranges. |
writeDB | Saving and loading 'refGenome' objects to and from SQLite databases. |
writeDB-method | Saving and loading 'refGenome' objects to and from SQLite databases. |
writeDB-methods | Saving and loading 'refGenome' objects to and from SQLite databases. |
+-method | Class '"geneList"' |
+-method | Class '"geneModel"' |
[-method | Class '"geneList"' |