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| $-method | BSgenome objects |
| as.list-method | BSgenome objects |
| available.genomes | Find available/installed genomes |
| available.SNPs | SNP injection |
| bsapply | bsapply |
| BSgenome | BSgenome objects |
| BSgenome-class | BSgenome objects |
| BSgenome-utils | BSgenome utilities |
| BSgenomeDataPkgSeed | The BSgenomeForge functions |
| BSgenomeDataPkgSeed-class | The BSgenomeForge functions |
| BSgenomeForge | The BSgenomeForge functions |
| BSParams | Class "BSParams" |
| BSParams-class | Class "BSParams" |
| class:BSgenome | BSgenome objects |
| class:BSgenomeDataPkgSeed | The BSgenomeForge functions |
| class:BSParams | Class "BSParams" |
| class:InjectSNPsHandler | SNP injection |
| class:SNPlocs | SNPlocs objects |
| coerce-method | Data on the genome |
| coerce-method | List of GenomeData objects |
| compatibleGenomes | SNPlocs objects |
| compatibleGenomes-method | SNPlocs objects |
| countPWM-method | BSgenome utilities |
| export-method | Export a BSgenome object as a FASTA or twoBit file |
| export-methods | Export a BSgenome object as a FASTA or twoBit file |
| forgeBSgenomeDataPkg | The BSgenomeForge functions |
| forgeBSgenomeDataPkg-method | The BSgenomeForge functions |
| forgeMasksFiles | The BSgenomeForge functions |
| forgeSeqFiles | The BSgenomeForge functions |
| forgeSeqlengthsFile | The BSgenomeForge functions |
| gdapply | Applies a function to elements of a GenomeData |
| gdapply-method | Applies a function to elements of a GenomeData |
| gdReduce | Reduces arguments to a single GenomeData instance |
| gdReduce-method | Reduces arguments to a single GenomeData instance |
| GenomeData | Data on the genome |
| GenomeData-class | Data on the genome |
| GenomeDataList | List of GenomeData objects |
| GenomeDataList-class | List of GenomeData objects |
| getBSgenome | Find available/installed genomes |
| getSeq-method | getSeq method for BSgenome objects |
| injectSNPs | SNP injection |
| injectSNPs-method | SNP injection |
| InjectSNPsHandler | SNP injection |
| InjectSNPsHandler-class | SNP injection |
| installed.genomes | Find available/installed genomes |
| installed.SNPs | SNP injection |
| length-method | BSgenome objects |
| masknames | BSgenome objects |
| masknames-method | BSgenome objects |
| matchPWM-method | BSgenome utilities |
| mseqnames | BSgenome objects |
| mseqnames-method | BSgenome objects |
| names-method | BSgenome objects |
| newSNPlocs | SNPlocs objects |
| organism-method | Data on the genome |
| organism-method | SNPlocs objects |
| provider-method | Data on the genome |
| provider-method | SNPlocs objects |
| providerVersion-method | Data on the genome |
| providerVersion-method | SNPlocs objects |
| referenceGenome | SNPlocs objects |
| referenceGenome-method | SNPlocs objects |
| releaseDate-method | SNPlocs objects |
| releaseName-method | SNPlocs objects |
| seqinfo-method | BSgenome objects |
| seqinfo-method | SNPlocs objects |
| seqinfo<--method | BSgenome objects |
| seqnames-method | SNPlocs objects |
| seqnames<--method | BSgenome objects |
| show-method | BSgenome objects |
| show-method | Data on the genome |
| show-method | SNPlocs objects |
| SNPcount | SNP injection |
| snpcount | SNPlocs objects |
| SNPcount-method | SNP injection |
| snpcount-method | SNPlocs objects |
| snpcount-method | SNP injection |
| snpid2alleles | SNPlocs objects |
| snpid2alleles-method | SNPlocs objects |
| snpid2grange | SNPlocs objects |
| snpid2grange-method | SNPlocs objects |
| snpid2loc | SNPlocs objects |
| snpid2loc-method | SNPlocs objects |
| SNPlocs | SNPlocs objects |
| snplocs | SNPlocs objects |
| SNPlocs-class | SNPlocs objects |
| SNPlocs-method | SNP injection |
| snplocs-method | SNPlocs objects |
| snplocs-method | SNP injection |
| SNPlocs_pkgname | SNP injection |
| SNPlocs_pkgname-method | SNP injection |
| sourceUrl | BSgenome objects |
| sourceUrl-method | BSgenome objects |
| species-method | SNPlocs objects |
| vcountPattern-method | BSgenome utilities |
| vcountPDict-method | BSgenome utilities |
| vmatchPattern-method | BSgenome utilities |
| vmatchPDict-method | BSgenome utilities |
| [[-method | BSgenome objects |
| [[<--method | BSgenome objects |