Infrastructure for Biostrings-based genome data packages


[Package List] [Top]

Documentation for package ‘BSgenome’ version 1.14.2

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

$,BSgenome-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:GenomeDescription GenomeDescription objects
coerce,GenomeData,data.frame-method Data on the genome
coerce,GenomeData,RangedData-method Data on the genome
coerce,GenomeData,RangesList-method Data on the genome
coerce,GenomeDataList,data.frame-method List of GenomeData objects
countPWM,BSgenome-method BSgenome utilities
forgeBSgenomeDataPkg The BSgenomeForge functions
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method The BSgenomeForge functions
forgeBSgenomeDataPkg,character-method The BSgenomeForge functions
forgeBSgenomeDataPkg,list-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,GenomeData,function-method Applies a function to elements of a GenomeData
gdapply,GenomeData,function-method Applies a function to elements of a GenomeData
gdApply,GenomeDataList,function-method Applies a function to elements of a GenomeData
gdapply,GenomeDataList,function-method Applies a function to elements of a GenomeData
gdreduce Reduces arguments to a single GenomeData instance
gdreduce,GenomeData-method Data on the genome
gdreduce,GenomeDataList-method List of GenomeData objects
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 getSeq
getSeq,BSgenome-method getSeq
injectSNPs SNP injection
injectSNPs,BSgenome-method SNP injection
installed.genomes Find available/installed genomes
installed.SNPs SNP injection
length,BSgenome-method BSgenome objects
masknames BSgenome objects
masknames,BSgenome-method BSgenome objects
matchPWM,BSgenome-method BSgenome utilities
mseqnames BSgenome objects
mseqnames,BSgenome-method BSgenome objects
names,BSgenome-method BSgenome objects
organism GenomeDescription objects
organism,GenomeData-method Data on the genome
organism,GenomeDescription-method GenomeDescription objects
provider GenomeDescription objects
provider,GenomeData-method Data on the genome
provider,GenomeDescription-method GenomeDescription objects
providerVersion GenomeDescription objects
providerVersion,GenomeData-method Data on the genome
providerVersion,GenomeDescription-method GenomeDescription objects
releaseDate GenomeDescription objects
releaseDate,GenomeDescription-method GenomeDescription objects
releaseName GenomeDescription objects
releaseName,GenomeDescription-method GenomeDescription objects
seqlengths BSgenome objects
seqlengths,BSgenome-method BSgenome objects
seqnames BSgenome objects
seqnames,BSgenome-method BSgenome objects
show,BSgenome-method BSgenome objects
show,GenomeData-method Data on the genome
show,GenomeDescription-method GenomeDescription objects
SNPcount SNP injection
SNPcount,BSgenome-method SNP injection
SNPlocs SNP injection
SNPlocs,BSgenome-method SNP injection
SNPlocs_pkgname SNP injection
SNPlocs_pkgname,BSgenome-method SNP injection
sourceUrl BSgenome objects
sourceUrl,BSgenome-method BSgenome objects
species GenomeDescription objects
species,GenomeDescription-method GenomeDescription objects
strand Accessing strand information
strand,character-method Accessing strand information
strand,DataTable-method Accessing strand information
strand,missing-method Accessing strand information
strand-methods Accessing strand information
vcountPattern,BSgenome-method BSgenome utilities
vmatchPattern,BSgenome-method BSgenome utilities
[[,BSgenome-method BSgenome objects
[[<-,BSgenome-method BSgenome objects