# Infrastructure for Biostrings-based genome data packages

## Documentation for package ‘BSgenome’ version 1.34.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-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