| 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"' |
| getGenePositions | Extract subsets of refGenome by gene-name. |
| getGenePositions-method | Extract subsets of refGenome by gene-name. |
| getGenePositions-methods | Extract subsets of refGenome by gene-name. |
| getGeneTable | Class '"ensemblGenome"' |
| getGeneTable-method | Class '"ensemblGenome"' |
| 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"' |
| getXref | Class '"ucscGenome"' |
| getXref-method | Class '"ucscGenome"' |
| getXref-methods | Class '"ucscGenome"' |
| initialize-method | Class '"refGenome"' |
| loadGenome | Saving and loading 'refGenome' objects |
| loadGenomeDb | Saving and loading 'refGenome' objects to and from SQLite databases. |
| overlap | overlap function |
| overlapJuncs | overlapJuncs function |
| 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"' |
| 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"' |
| 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. |