API for Przemol/mirrors-bioc-BSgenome
Infrastructure for Biostrings-based genome data packages

Global functions
$,BSgenome-method Man page
BSParams Man page
BSParams-class Man page
BSgenome Man page Man page Source code
BSgenome-class Man page
BSgenome-utils Man page
BSgenomeDataPkgSeed Man page Source code
BSgenomeDataPkgSeed-class Man page
BSgenomeForge Man page
FastaNamedSequences Source code
GenomeData Man page Source code
GenomeData-class Man page
GenomeDataList Man page Source code
GenomeDataList-class Man page
GenomeDescription Man page Source code
GenomeDescription-class Man page
InjectSNPsHandler Man page Source code
InjectSNPsHandler-class Man page
MaskedBSgenome Source code
MaskedBSgenomeDataPkgSeed Source code
RdaNamedSequences Source code
SNPcount Man page
SNPcount,BSgenome-method Man page
SNPcount,InjectSNPsHandler-method Man page
SNPlocs Man page
SNPlocs,BSgenome-method Man page
SNPlocs,InjectSNPsHandler-method Man page
SNPlocsAsGranges Source code
SNPlocs_pkgname Man page
SNPlocs_pkgname,BSgenome-method Man page
SNPlocs_pkgname,InjectSNPsHandler-method Man page
[[,BSgenome-method Man page
[[<-,BSgenome-method Man page
available.SNPs Man page Source code
available.genomes Man page Source code
bsapply Man page Source code
bsgenomeName Man page
bsgenomeName,GenomeDescription-method Man page
check.seqname_translation_table Source code
class:BSParams Man page
class:BSgenome Man page
class:BSgenomeDataPkgSeed Man page
class:GenomeDescription Man page
class:InjectSNPsHandler Man page
coerce,GenomeData,RangedData-method Man page
coerce,GenomeData,RangesList-method Man page
coerce,GenomeData,data.frame-method Man page
coerce,GenomeDataList,data.frame-method Man page
countPWM,BSgenome-method Man page
create_object Source code
dropUnusedGRangesSeqnamesLevels Source code
extractFromBSgenomeMultipleSequences Source code
extractFromBSgenomeSingleSequences Source code
forge.AGAPSmask Source code
forge.AMBmask Source code
forge.RMmask Source code
forge.TRFmask Source code
forgeBSgenomeDataPkg Man page
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method Man page
forgeBSgenomeDataPkg,character-method Man page
forgeBSgenomeDataPkg,list-method Man page
forgeFastaRzFile Source code
forgeMasksFile Source code
forgeMasksFiles Man page Source code
forgeRdaSeqFile Source code
forgeSeqFiles Man page Source code
forgeSeqlengthsFile Man page Source code
gdReduce Man page
gdReduce,GenomeData-method Man page
gdReduce,GenomeDataList-method Man page
gdapply Man page
gdapply,GenomeData,function-method Man page
gdapply,GenomeDataList,function-method Man page
gdreduce Man page Source code
get.seqname_translation_table Source code
getBSgenome Man page Source code
getBSgenomeObjectFromInstalledPkgname Source code
getBSgenomeSequence Source code
getDataAnnotationContribUrl Source code
getInstalledPkgnameFromProviderVersion Source code
getMasksObjname Source code
getOneSeqFromBSgenomeMultipleSequences Source code
getSeq,BSgenome-method Man page
getSeqSrcpaths Source code
getSeqlengths Source code
get_SNPlocs_data Source code
get_rsid_offsets Source code
get_seqlength Source code
get_ufsnplocs Source code
has_BSgenome_prefix Source code
injectSNPs Man page
injectSNPs,BSgenome-method Man page
installed.SNPs Man page Source code
installed.genomes Man page Source code
length,BSgenome-method Man page
listOfDNAStringToDNAStringSet Source code
loadBSgenomeSequence Source code
loadSubseqsFromCircularSequence Source code
loadSubseqsFromStrandedSequence Source code
load_raw_snplocs Source code
load_rsids Source code
makeBSgenomeSeqinfo Source code
makeS4FromList Source code
masknames Man page
masknames,BSgenome-method Man page
matchPWM,BSgenome-method Man page
mseqnames Man page
mseqnames,BSgenome-method Man page
names,BSgenome-method Man page
newGRangesFromNamedRanges Source code
newGRangesFromNamedRangesList Source code
newLinkToCachedObject Source code
newSNPlocs Source code
normGetSeqArgs Source code
normargSnpid Source code
normargStrand Source code
organism Man page
organism,GenomeData-method Man page
organism,GenomeDescription-method Man page
provider Man page
provider,GenomeData-method Man page
provider,GenomeDescription-method Man page
providerVersion Man page
providerVersion,GenomeData-method Man page
providerVersion,GenomeDescription-method Man page
read.dcf2 Source code
readSeedFile Source code
releaseDate Man page
releaseDate,GenomeDescription-method Man page
releaseName Man page
releaseName,GenomeDescription-method Man page
removeCommentLines Source code
saveObject Source code
seqinfo,BSgenome-method Man page
seqinfo,GenomeDescription-method Man page
seqinfo<-,BSgenome-method Man page
seqnames<-,BSgenome-method Man page
show,BSgenome-method Man page
show,GenomeData-method Man page
show,GenomeDescription-method Man page
showGenomeDescription Source code
snpid2rowidx Source code
sourceUrl Man page
sourceUrl,BSgenome-method Man page
species Man page
species,GenomeDescription-method Man page
splitNameParts Source code
starfreeStrand Source code
stopOnAvailablePkg Source code
stopOnMoreThanOneAvailablePkg Source code
toGRanges Source code
vcountPDict,BSgenome-method Man page
vcountPattern,BSgenome-method Man page
vmatchPDict,BSgenome-method Man page
vmatchPattern,BSgenome-method Man page
Przemol/mirrors-bioc-BSgenome documentation built on May 9, 2017, 8:39 p.m.