# Software infrastructure for efficient representation of full genomes and their SNPs

## Documentation for package ‘BSgenome’ version 1.56.0

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

## Help Pages

A B C D E F G H I L M N O P R S U V W X misc

## -- A --

alphabetFrequency-method | BSgenomeViews objects
as.character-method | BSgenomeViews objects
as.data.frame-method | BSgenomeViews objects
as.list-method | BSgenome objects
available.genomes | Find available/installed genomes
available.SNPs | SNP injection

## -- B --

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
BSgenomeViews | BSgenomeViews objects
BSgenomeViews-class | BSgenomeViews objects
BSParams | Class "BSParams"
BSParams-class | Class "BSParams"

## -- C --

class:BSgenome | BSgenome objects
class:BSgenomeDataPkgSeed | The BSgenomeForge functions
class:BSgenomeViews | BSgenomeViews objects
class:BSParams | Class "BSParams"
class:InjectSNPsHandler | SNP injection
class:ODLT_SNPlocs | SNPlocs objects
class:OldFashionSNPlocs | SNPlocs objects
class:SNPlocs | SNPlocs objects
class:XtraSNPlocs | XtraSNPlocs objects
coerce-method | BSgenomeViews objects
colnames-method | XtraSNPlocs objects
commonName-method | SNPlocs objects
commonName-method | XtraSNPlocs objects
compatibleGenomes | SNPlocs objects
compatibleGenomes-method | SNPlocs objects
consensusMatrix-method | BSgenomeViews objects
consensusString-method | BSgenomeViews objects
countPWM-method | BSgenome utilities

## -- D --

dim-method | XtraSNPlocs objects

## -- E --

elementNROWS-method | BSgenomeViews objects
end-method | BSgenomeViews objects
export-method | Export a BSgenome object as a FASTA or twoBit file
export-methods | Export a BSgenome object as a FASTA or twoBit file
extractROWS-method | BSgenomeViews objects

## -- F --

forgeBSgenomeDataPkg | The BSgenomeForge functions
forgeBSgenomeDataPkg-method | The BSgenomeForge functions
forgeMasksFiles | The BSgenomeForge functions
forgeSeqFiles | The BSgenomeForge functions
forgeSeqlengthsFile | The BSgenomeForge functions

## -- G --

getBSgenome | Find available/installed genomes
getListElement-method | BSgenomeViews objects
getSeq | getSeq methods for BSgenome and XStringSet objects
getSeq-method | getSeq methods for BSgenome and XStringSet objects
granges-method | BSgenomeViews objects

## -- H --

hasOnlyBaseLetters-method | BSgenomeViews objects

## -- I --

inferRefAndAltAlleles | SNPlocs 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

## -- L --

length-method | BSgenome objects
length-method | BSgenomeViews objects
letterFrequency-method | BSgenomeViews objects

## -- M --

masknames | BSgenome objects
masknames-method | BSgenome objects
matchPWM-method | BSgenome utilities
mseqnames | BSgenome objects
mseqnames-method | BSgenome objects

## -- N --

names-method | BSgenome objects
names-method | BSgenomeViews objects
nchar-method | BSgenomeViews objects
newSNPlocs | SNPlocs objects
newXtraSNPlocs | XtraSNPlocs objects
new_ODLT_SNPlocs | SNPlocs objects
nucleotideFrequencyAt-method | BSgenomeViews objects

## -- O --

ODLT_SNPlocs | SNPlocs objects
ODLT_SNPlocs-class | SNPlocs objects
OldFashionSNPlocs | SNPlocs objects
OldFashionSNPlocs-class | SNPlocs objects
oligonucleotideFrequency-method | BSgenomeViews objects
organism-method | SNPlocs objects
organism-method | XtraSNPlocs objects

## -- P --

provider-method | SNPlocs objects
provider-method | XtraSNPlocs objects
providerVersion-method | SNPlocs objects
providerVersion-method | XtraSNPlocs objects

## -- R --

ranges-method | BSgenomeViews objects
referenceGenome | SNPlocs objects
referenceGenome-method | SNPlocs objects
referenceGenome-method | XtraSNPlocs objects
releaseDate-method | SNPlocs objects
releaseDate-method | XtraSNPlocs objects
releaseName-method | SNPlocs objects
releaseName-method | XtraSNPlocs objects

## -- S --

seqinfo-method | BSgenome objects
seqinfo-method | BSgenomeViews objects
seqinfo-method | SNPlocs objects
seqinfo-method | XtraSNPlocs objects
seqinfo<--method | BSgenome objects
seqnames-method | BSgenomeViews objects
seqnames-method | SNPlocs objects
seqnames-method | XtraSNPlocs objects
seqnames<--method | BSgenome objects
seqtype-method | BSgenomeViews objects
show-method | BSgenome objects
show-method | BSgenomeViews objects
show-method | SNPlocs objects
show-method | XtraSNPlocs objects
snpcount | SNPlocs objects
snpcount-method | SNPlocs objects
snpcount-method | XtraSNPlocs 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 | SNPlocs objects
snplocs-method | SNP injection
SNPlocs_pkgname | SNP injection
SNPlocs_pkgname-method | SNP injection
snpsById | SNPlocs objects
snpsById-method | SNPlocs objects
snpsById-method | XtraSNPlocs objects
snpsByOverlaps | SNPlocs objects
snpsByOverlaps-method | SNPlocs objects
snpsByOverlaps-method | XtraSNPlocs objects
snpsBySeqname | SNPlocs objects
snpsBySeqname-method | SNPlocs objects
snpsBySeqname-method | XtraSNPlocs objects
sourceUrl | BSgenome objects
sourceUrl-method | BSgenome objects
species-method | XtraSNPlocs objects
start-method | BSgenomeViews objects
strand-method | BSgenomeViews objects
subject-method | BSgenomeViews objects

## -- U --

uniqueLetters-method | BSgenomeViews objects
unlist-method | BSgenomeViews objects

## -- V --

vcountPattern-method | BSgenome utilities
vcountPDict-method | BSgenome utilities
Views-method | BSgenomeViews objects
vmatchPattern-method | BSgenome utilities
vmatchPDict-method | BSgenome utilities

## -- W --

width-method | BSgenomeViews objects
writeBSgenomeToFasta | Export a BSgenome object as a FASTA or twoBit file
writeBSgenomeToTwobit | Export a BSgenome object as a FASTA or twoBit file

## -- X --

XtraSNPlocs | XtraSNPlocs objects
XtraSNPlocs-class | XtraSNPlocs objects

## -- misc --

$-method | BSgenome objects
[-method | getSeq methods for BSgenome and XStringSet objects
[[-method | BSgenome objects