Infrastructure for Biostrings-based genome data packages


[Up] [Top]

Documentation for package ‘BSgenome’ version 1.34.1

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