Bioconductor/BSgenome
Software infrastructure for efficient representation of full genomes and their SNPs

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365
Source code
19
Man pages
12
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Bioconductor/BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs
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API

API for Bioconductor/BSgenome
Software infrastructure for efficient representation of full genomes and their SNPs

Global functions
$,BSgenome-method Man page
.OnDiskLongTable_old_blockidx2blockname Source code
.OnDiskLongTable_old_check_breakpoints Source code
.OnDiskLongTable_old_check_dirpath Source code
.OnDiskLongTable_old_check_rowids Source code
.OnDiskLongTable_old_colidx2dirname Source code
.OnDiskLongTable_old_colidx2dirpath Source code
.OnDiskLongTable_old_get_nrow_from_breakpoints Source code
.SNPlocsAsGRanges Source code
.XtraSNPlocs_check_user_supplied_columns Source code
.XtraSNPlocs_get_DF_for_ids Source code
.XtraSNPlocs_get_DF_for_seqnames Source code
.XtraSNPlocs_get_physical_from_user_supplied_columns Source code
.append_batch_to_OnDiskLongTable_old Source code
.append_df_to_OnDiskLongTable Source code
.as.data.frame.BSgenomeViews Source code
.as_DataFrame Source code
.as_GPos Source code
.as_data.frame Source code
.as_naked_GPos Source code
.batch_physname Source code
.block_physname Source code
.breakpoints2offsets Source code Source code
.check.seqname_translation_table Source code
.check_OnDiskLongTable_dirpath Source code
.check_OnDiskLongTable_rowids Source code
.check_getListElement_index Source code
.check_new2old_and_new_seqinfo Source code
.col_physname Source code
.create_and_initialize_column_dir Source code
.create_object Source code
.drop_unused_seqlevels Source code
.extractAt_BSgenome Source code
.extractFromBSgenomeMultipleSequences Source code
.extractFromBSgenomeSingleSequences Source code
.extract_dna_from_BSgenomeViews Source code
.extract_genome_sequences_at Source code
.fast_extract_genome_sequences_at Source code
.friendly_read_object Source code
.from_BSgenomeViews_to_DNAStringSet Source code
.get.seqname_translation_table Source code
.getBSgenomeObjectFromInstalledPkgname Source code
.getBSgenomeSequence Source code
.getInstalledPkgnameFromGenome Source code
.getListElement_BSgenomeViews Source code
.getOneSeqFromBSgenomeMultipleSequences Source code
.get_GPos_by_seqname_from_SNPlocs Source code
.get_GRanges_by_id_from_XtraSNPlocs Source code
.get_GRanges_by_seqname_from_XtraSNPlocs Source code
.get_OnDiskLongTable_nrow_from_breakpoints Source code
.get_SNPlocs_data Source code
.get_blocks_from_column Source code
.get_rowids_filepaths Source code
.get_rsid_offsets Source code
.get_seqlength Source code
.get_snpcount_from_blocksizes Source code
.get_ufsnplocs Source code
.get_values_from_column Source code
.has_BSgenome_prefix Source code
.keep_snps_packages Source code
.listOfDNAStringToDNAStringSet Source code
.loadBSgenomeSequence Source code
.loadSubseqsFromCircularSequence Source code
.load_block Source code
.load_object Source code
.load_raw_snplocs Source code
.load_rowids Source code
.load_rsids Source code
.makeNakedMatFromBSgenomeViews Source code
.make_BSgenome_seqinfo Source code
.make_filepath Source code
.newGRangesFromNamedRanges Source code
.newGRangesFromNamedRangesList Source code
.newLinkToCachedObject Source code
.normGetSeqArgs Source code
.normargStrand Source code
.normarg_batch_labels Source code
.normarg_batchidx Source code
.normarg_batchsize Source code
.normarg_blocksize Source code
.normarg_colidx Source code Source code
.normarg_columns Source code
.normarg_rowidx Source code Source code
.normarg_snpid Source code
.print_BSgenome_metadata Source code
.read_OnDiskLongTable_batch_column Source code
.read_OnDiskLongTable_block Source code
.read_OnDiskLongTable_column Source code
.read_object Source code
.read_seqlengths_from_file Source code
.remove_dirs Source code Source code
.remove_file Source code
.remove_files Source code
.reverseComplement_PDict Source code
.rowids2rowidx Source code
.rowidx2rowkeys Source code Source code
.save_object Source code
.save_rowids_in_chunks Source code
.seqnames2batchidx Source code
.set_BSgenome_seqinfo Source code
.show_BSgenome Source code
.slow_extract_genome_sequences_at Source code
.snpid2alleles_OldFashionSNPlocs Source code
.snpid2grange_OldFashionSNPlocs Source code
.snpid2loc_OldFashionSNPlocs Source code
.snpid2rowidx Source code
.snpsById_ODLT_SNPlocs Source code
.snpsById_OldFashionSNPlocs Source code
.snpsByOverlaps_ODLT_SNPlocs Source code
.snpsByOverlaps_OldFashionSNPlocs Source code
.snpsBySeqname_ODLT_SNPlocs Source code
.snpsBySeqname_OldFashionSNPlocs Source code
.splitNameParts Source code
.starfreeStrand Source code
.stopOnAvailablePkg Source code
.stopOnMoreThanOneAvailablePkg Source code
.toGRanges Source code
.to_DataFrame Source code
.valid_OnDiskLongTable Source code
.valid_OnDiskLongTable_breakpoints Source code
.valid_OnDiskLongTable_dirpath Source code
.valid_OnDiskLongTable_header Source code
.valid_OnDiskLongTable_spatial_index Source code
.write_OnDiskLongTable_block Source code
.write_OnDiskLongTable_column Source code
.write_column Source code
.write_object Source code
.write_zero_row_OnDiskLongTable Source code
.write_zero_row_OnDiskLongTable_old Source code
AdvancedBSgenomeForge Man page
BSParams Man page
BSParams-class Man page
BSgenome Man page Man page Source code
BSgenome-class Man page
BSgenome-utils Man page
BSgenomeViews Man page Source code
BSgenomeViews-class Man page
FastaNamedSequences Source code
InjectSNPsHandler Man page Source code
InjectSNPsHandler-class Man page
MaskedBSgenome Source code
ODLT_SNPlocs Man page
ODLT_SNPlocs-class Man page
OldFashionSNPlocs Man page
OldFashionSNPlocs-class Man page
OnDiskLongTable Source code
OnDiskLongTable_old Source code
OnDiskNamedSequences Source code
RdaNamedSequences Source code
RdsNamedSequences Source code
SNPlocs Man page
SNPlocs-class Man page
SNPlocs_pkgname Man page
SNPlocs_pkgname,BSgenome-method Man page
SNPlocs_pkgname,InjectSNPsHandler-method Man page
TwobitNamedSequences Source code
Views,BSgenome-method Man page
XtraSNPlocs Man page
XtraSNPlocs-class Man page
[,XStringSet,GRangesList-method Man page
[,XStringSet,GenomicRanges-method Man page
[[,BSgenome-method Man page
alphabetFrequency,BSgenomeViews-method Man page
as.character,BSgenomeViews-method Man page
as.data.frame,BSgenomeViews-method Man page
as.data.frame.BSgenomeViews Source code
as.list,BSgenome-method Man page
available.SNPs Man page Source code
available.genomes Man page Source code
bsapply Man page Source code
bsgenomeName,BSgenome-method Man page
call_fun_in_BSgenomeForge Source code
class:BSParams Man page
class:BSgenome Man page
class:BSgenomeViews Man page
class:InjectSNPsHandler Man page
class:ODLT_SNPlocs Man page
class:OldFashionSNPlocs Man page
class:SNPlocs Man page
class:XtraSNPlocs Man page
coerce,BSgenome,GenomeDescription-method Man page
coerce,BSgenomeViews,DNAStringSet-method Man page
coerce,BSgenomeViews,XStringSet-method Man page
colnames,XtraSNPlocs-method Man page
commonName,BSgenome-method Man page
commonName,SNPlocs-method Man page
commonName,XtraSNPlocs-method Man page
compatibleGenomes Man page
compatibleGenomes,SNPlocs-method Man page
consensusMatrix,BSgenomeViews-method Man page
consensusString,BSgenomeViews-method Man page
countPWM,BSgenome-method Man page
decode_bytes_as_letters Source code
dim,XtraSNPlocs-method Man page
elementNROWS,BSgenomeViews-method Man page
encode_letters_as_bytes Source code
end,BSgenomeViews-method Man page
export,BSgenome,FastaFile,ANY-method Man page
export,BSgenome,TwoBitFile,ANY-method Man page
export-methods Man page
extractROWS,BSgenomeViews-method Man page
extract_rowids Source code
forgeBSgenomeDataPkg Man page Source code
forgeMaskedBSgenomeDataPkg Man page Source code
forgeMasksFiles Man page Source code
forgeSeqFiles Man page Source code
forgeSeqlengthsRdaFile Man page Source code
forgeSeqlengthsRdsFile Man page Source code
getBSgenome Man page Source code
getBatchesByOverlapsFromOnDiskLongTable Source code
getBatchesBySeqnameFromOnDiskLongTable Source code
getBatchesFromOnDiskLongTable Source code
getBatchesFromOnDiskLongTable_old Source code
getListElement,BSgenomeViews-method Man page
getRowsByIdFromOnDiskLongTable Source code
getRowsByIndexFromOnDiskLongTable_old Source code
getRowsFromOnDiskLongTable Source code
getSeq Man page
getSeq,BSgenome-method Man page
getSeq,XStringSet-method Man page
get_data_annotation_contrib_url Source code
get_rowids_env Source code
get_rowids_env_old Source code
granges,BSgenomeViews-method Man page
hasOnlyBaseLetters,BSgenomeViews-method Man page
ids2rowids Source code
inferRefAndAltAlleles Man page 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
length,BSgenomeViews-method Man page
letterFrequency,BSgenomeViews-method Man page
loadSubseqsFromStrandedSequence Source code
load_package_gracefully Source code
lookup_rowids Source code
masknames Man page
masknames,BSgenome-method Man page
masknames,MaskedBSgenome-method Man page
matchPWM,BSgenome-method Man page
mseqnames Man page
mseqnames,BSgenome-method Man page
names,BSgenome-method Man page
names,BSgenomeViews-method Man page
nchar,BSgenomeViews-method Man page
newSNPlocs Man page Source code
newXtraSNPlocs Man page Source code
new_ODLT_SNPlocs Man page Source code
normarg_ranges Source code
nucleotideFrequencyAt,BSgenomeViews-method Man page
oligonucleotideFrequency,BSgenomeViews-method Man page
organism,BSgenome-method Man page
organism,SNPlocs-method Man page
organism,XtraSNPlocs-method Man page
provider,BSgenome-method Man page
provider,SNPlocs-method Man page
provider,XtraSNPlocs-method Man page
providerVersion,BSgenome-method Man page
providerVersion,SNPlocs-method Man page
providerVersion,XtraSNPlocs-method Man page
ranges,BSgenomeViews-method Man page
read_seqinfo_table Source code
referenceGenome Man page
referenceGenome,SNPlocs-method Man page
referenceGenome,XtraSNPlocs-method Man page
releaseDate,BSgenome-method Man page
releaseDate,SNPlocs-method Man page
releaseDate,XtraSNPlocs-method Man page
releaseName Man page
releaseName,SNPlocs-method Man page
releaseName,XtraSNPlocs-method Man page
rowids2rowidx Source code
saveAsOnDiskLongTable_old Source code
saveRowidsForOnDiskLongTable_old Source code
seqinfo,BSgenome-method Man page
seqinfo,BSgenomeViews-method Man page
seqinfo,SNPlocs-method Man page
seqinfo,XtraSNPlocs-method Man page
seqinfo<-,BSgenome-method Man page
seqnames,BSgenome-method Man page
seqnames,BSgenomeViews-method Man page
seqnames,SNPlocs-method Man page
seqnames,XtraSNPlocs-method Man page
seqnames<-,BSgenome-method Man page
seqtype,BSgenomeViews-method Man page
show,BSgenome-method Man page
show,BSgenomeViews-method Man page
show,SNPlocs-method Man page
show,XtraSNPlocs-method Man page
showBSgenomeViews Source code
snpcount Man page
snpcount,BSgenome-method Man page
snpcount,InjectSNPsHandler-method Man page
snpcount,ODLT_SNPlocs-method Man page
snpcount,OldFashionSNPlocs-method Man page
snpcount,SNPlocs-method Man page
snpcount,XtraSNPlocs-method Man page
snplocs Man page
snplocs,BSgenome-method Man page
snplocs,InjectSNPsHandler-method Man page
snplocs,ODLT_SNPlocs-method Man page
snplocs,OldFashionSNPlocs-method Man page
snplocs,SNPlocs-method Man page
snpsById Man page
snpsById,ODLT_SNPlocs-method Man page
snpsById,OldFashionSNPlocs-method Man page
snpsById,SNPlocs-method Man page
snpsById,XtraSNPlocs-method Man page
snpsByOverlaps Man page
snpsByOverlaps,ODLT_SNPlocs-method Man page
snpsByOverlaps,OldFashionSNPlocs-method Man page
snpsByOverlaps,SNPlocs-method Man page
snpsByOverlaps,XtraSNPlocs-method Man page
snpsBySeqname Man page
snpsBySeqname,ODLT_SNPlocs-method Man page
snpsBySeqname,OldFashionSNPlocs-method Man page
snpsBySeqname,SNPlocs-method Man page
snpsBySeqname,XtraSNPlocs-method Man page
sourceUrl Man page
sourceUrl,BSgenome-method Man page
species,XtraSNPlocs-method Man page
splitLRgranges Source code
splitLRranges Source code
start,BSgenomeViews-method Man page
strand,BSgenomeViews-method Man page
subject,BSgenomeViews-method Man page
uniqueLetters,BSgenomeViews-method Man page
unlist,BSgenomeViews-method Man page
vcountPDict,BSgenome-method Man page
vcountPattern,BSgenome-method Man page
vmatchPDict,BSgenome-method Man page
vmatchPattern,BSgenome-method Man page
width,BSgenomeViews-method Man page
writeBSgenomeToFasta Man page Source code
writeBSgenomeToTwobit Man page Source code
writeOnDiskLongTable Source code
writeOnDiskLongTableRowids Source code
Bioconductor/BSgenome documentation built on April 1, 2024, 5:50 p.m.

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