/usr/lib/R/site-library/BSgenome/NAMESPACE is in r-bioc-bsgenome 1.32.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import(BiocGenerics)
import(IRanges)
import(GenomicRanges)
import(XVector)
import(Biostrings)
import(Rsamtools)
exportClasses(
GenomeDescription,
SNPlocs,
InjectSNPsHandler,
BSgenome, MaskedBSgenome,
GenomeData, GenomeDataList,
## BSgenomeForge classes:
BSgenomeDataPkgSeed
)
export(
## Non-generic functions:
GenomeDescription,
newSNPlocs,
BSgenome, MaskedBSgenome,
installed.genomes, available.genomes, getBSgenome,
installed.SNPs, available.SNPs,
bsapply,
GenomeData, GenomeDataList,
## Generic functions:
organism, species, provider, providerVersion,
releaseDate, releaseName, bsgenomeName,
referenceGenome, compatibleGenomes,
snpcount, snplocs,
snpid2loc, snpid2alleles, snpid2grange,
sourceUrl,
SNPlocs, SNPlocs_pkgname, SNPcount,
mseqnames,
masknames,
injectSNPs,
gdapply,
gdReduce, gdreduce,
## BSgenomeForge functions:
forgeSeqlengthsFile,
forgeSeqFiles,
forgeMasksFiles,
forgeBSgenomeDataPkg,
forgeMaskedBSgenomeDataPkg
)
exportMethods(
## Methods for generics defined elsewhere:
names, show, length, "[[", "$", score,
getSeq, matchPWM, countPWM, vmatchPattern, vcountPattern,
## Methods for generics defined in this package:
organism, species, provider, providerVersion,
releaseDate, releaseName, bsgenomeName,
seqinfo, "seqinfo<-", seqnames,
referenceGenome, compatibleGenomes,
snpcount, snplocs,
snpid2loc, snpid2alleles, snpid2grange,
sourceUrl,
SNPlocs, SNPlocs_pkgname, SNPcount,
mseqnames,
masknames,
injectSNPs,
gdapply,
gdReduce,
## BSgenomeForge methods:
forgeBSgenomeDataPkg
)
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