/usr/lib/R/site-library/BSgenome/NAMESPACE is in r-bioc-bsgenome 1.30.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 | import(methods)
import(BiocGenerics)
import(IRanges)
import(GenomicRanges)
import(Biostrings)
exportClasses(
GenomeDescription,
SNPlocs,
InjectSNPsHandler,
BSgenome,
GenomeData, GenomeDataList,
## BSgenomeForge classes:
BSgenomeDataPkgSeed
)
export(
## Non-generic functions:
installed.genomes, available.genomes,
GenomeDescription,
newSNPlocs,
BSgenome,
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, gdApply,
gdReduce, gdreduce,
## BSgenomeForge functions:
forgeSeqlengthsFile,
forgeSeqFiles,
forgeMasksFiles,
forgeBSgenomeDataPkg
)
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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