Software infrastructure for efficient representation of full genomes and their SNPs

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Documentation for package ‘BSgenome’ version 1.62.0

• 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
bsgenomeName-method	BSgenome objects
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	BSgenome objects
coerce-method	BSgenomeViews objects
colnames-method	XtraSNPlocs objects
commonName-method	BSgenome 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
forgeSeqlengthsRdaFile	The BSgenomeForge functions
forgeSeqlengthsRdsFile	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	BSgenome objects
organism-method	SNPlocs objects
organism-method	XtraSNPlocs objects

-- P --

provider-method	BSgenome objects
provider-method	SNPlocs objects
provider-method	XtraSNPlocs objects
providerVersion-method	BSgenome 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	BSgenome objects
releaseDate-method	SNPlocs objects
releaseDate-method	XtraSNPlocs objects
releaseName-method	BSgenome 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	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