Infrastructure for Biostrings-based genome data packages


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Documentation for package ‘BSgenome’ version 1.30.0

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$-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
bsgenomeName GenomeDescription objects
bsgenomeName-method GenomeDescription objects
BSParams Class "BSParams"
BSParams-class Class "BSParams"
class:BSgenome BSgenome objects
class:BSgenomeDataPkgSeed The BSgenomeForge functions
class:BSParams Class "BSParams"
class:GenomeDescription GenomeDescription objects
class:InjectSNPsHandler SNP injection
coerce-method Data on the genome
coerce-method List of GenomeData objects
countPWM-method BSgenome utilities
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 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 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
GenomeDescription GenomeDescription objects
GenomeDescription-class GenomeDescription objects
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
organism GenomeDescription objects
organism-method Data on the genome
organism-method GenomeDescription objects
provider GenomeDescription objects
provider-method Data on the genome
provider-method GenomeDescription objects
providerVersion GenomeDescription objects
providerVersion-method Data on the genome
providerVersion-method GenomeDescription objects
releaseDate GenomeDescription objects
releaseDate-method GenomeDescription objects
releaseName GenomeDescription objects
releaseName-method GenomeDescription objects
seqinfo-method BSgenome objects
seqinfo-method GenomeDescription objects
seqinfo<--method BSgenome objects
seqnames<--method BSgenome objects
show-method BSgenome objects
show-method Data on the genome
show-method GenomeDescription objects
SNPcount SNP injection
SNPcount-method SNP injection
SNPlocs SNP injection
SNPlocs-method SNP injection
SNPlocs_pkgname SNP injection
SNPlocs_pkgname-method SNP injection
sourceUrl BSgenome objects
sourceUrl-method BSgenome objects
species GenomeDescription objects
species-method GenomeDescription objects
vcountPattern-method BSgenome utilities
vcountPDict-method BSgenome utilities
vmatchPattern-method BSgenome utilities
vmatchPDict-method BSgenome utilities
[[-method BSgenome objects
[[<--method BSgenome objects