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

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
BSgenomeViews Man page Source code
BSgenomeViews-class Man page
FastaNamedSequences Source code
InjectSNPsHandler Man page Source code
InjectSNPsHandler-class Man page
MaskedBSgenome Source code
MaskedBSgenomeDataPkgSeed 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
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
RdaNamedSequences Source code
SNPlocs Man page
SNPlocs-class Man page
SNPlocsAsGRanges Source code
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
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
[,XStringSet,GRangesList-method Man page
[,XStringSet,GenomicRanges-method Man page
[[,BSgenome-method Man page
alphabetFrequency,BSgenomeViews-method Man page
append_batch_to_OnDiskLongTable_old Source code
append_df_to_OnDiskLongTable Source code
as.character,BSgenomeViews-method Man page
as.data.frame,BSgenomeViews-method Man page
as.data.frame.BSgenomeViews Source code Source code
as.list,BSgenome-method Man page
as_DataFrame Source code
as_GPos Source code
as_data.frame Source code
as_naked_GRanges Source code
available.SNPs Man page Source code
available.genomes Man page Source code
batch_physname Source code
block_physname Source code
breakpoints2offsets Source code Source code
bsapply Man page Source code
check.seqname_translation_table Source code
check_OnDiskLongTable_dirpath Source code
check_OnDiskLongTable_rowids Source code
class:BSParams Man page
class:BSgenome Man page
class:BSgenomeDataPkgSeed 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,BSgenomeViews,DNAStringSet-method Man page
coerce,BSgenomeViews,XStringSet-method Man page
col_physname Source code
colnames,XtraSNPlocs-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
copySeqFile Source code
countPWM,BSgenome-method Man page
create_and_initialize_column_dir Source code
create_object Source code
decode_bytes_as_letters Source code
dim,XtraSNPlocs-method Man page
drop_unused_seqlevels Source code
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
extractFromBSgenomeMultipleSequences Source code
extractFromBSgenomeSingleSequences Source code
extractROWS,BSgenomeViews-method Man page
extract_dna_from_BSgenomeViews 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
forgeFastaRzFileFromFastaFiles Source code
forgeMasksFile Source code
forgeMasksFiles Man page Source code
forgeRdaSeqFile Source code
forgeSeqFiles Man page Source code
forgeSeqlengthsFile Man page Source code
forgeTwobitFileFromFastaFiles Source code
friendly_read_object Source code
from_BSgenomeViews_to_DNAStringSet Source code
get.seqname_translation_table Source code
getBSgenome Man page Source code
getBSgenomeObjectFromInstalledPkgname Source code
getBSgenomeSequence Source code
getBatchesByOverlapsFromOnDiskLongTable Source code
getBatchesBySeqnameFromOnDiskLongTable Source code
getBatchesFromOnDiskLongTable Source code
getBatchesFromOnDiskLongTable_old Source code
getInstalledPkgnameFromProviderVersion Source code
getListElement,BSgenomeViews-method Man page
getListElement_BSgenomeViews Source code
getMasksObjname Source code
getOneSeqFromBSgenomeMultipleSequences Source code
getRowsByIdFromOnDiskLongTable Source code
getRowsByIdFromOnDiskLongTable_old Source code
getRowsByIndexFromOnDiskLongTable_old Source code
getRowsFromOnDiskLongTable Source code
getSeq Man page
getSeq,BSgenome-method Man page
getSeq,XStringSet-method Man page
getSeqSrcpaths Source code
getSeqlengths 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_data_annotation_contrib_url Source code
get_rowids_path 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
granges,BSgenomeViews-method Man page
hasOnlyBaseLetters,BSgenomeViews-method Man page
has_BSgenome_prefix Source code
ids2rowids Source code
injectSNPs Man page
injectSNPs,BSgenome-method Man page
installed.SNPs Man page Source code
installed.genomes Man page Source code
keep_snps_packages Source code
length,BSgenome-method Man page
length,BSgenomeViews-method Man page
letterFrequency,BSgenomeViews-method Man page
listOfDNAStringToDNAStringSet Source code
loadBSgenomeSequence Source code
loadSubseqsFromCircularSequence Source code
loadSubseqsFromStrandedSequence Source code
load_block Source code
load_object Source code
load_raw_snplocs Source code
load_rsids Source code
makeBSgenomeSeqinfo Source code
makeNakedMatFromBSgenomeViews Source code
makeS4FromList Source code
make_filepath 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
names,BSgenomeViews-method Man page
nchar,BSgenomeViews-method Man page
newGRangesFromNamedRanges Source code
newGRangesFromNamedRangesList Source code
newLinkToCachedObject Source code
newSNPlocs Man page Source code
newXtraSNPlocs Man page Source code
new_ODLT_SNPlocs Man page 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_ranges Source code
normarg_rowidx Source code Source code
normarg_snpid Source code
nucleotideFrequencyAt,BSgenomeViews-method Man page
oligonucleotideFrequency,BSgenomeViews-method Man page
organism,SNPlocs-method Man page
organism,XtraSNPlocs-method Man page
provider,SNPlocs-method Man page
provider,XtraSNPlocs-method Man page
providerVersion,SNPlocs-method Man page
providerVersion,XtraSNPlocs-method Man page
ranges,BSgenomeViews-method Man page
read.dcf2 Source code
readSeedFile Source code
read_OnDiskLongTable_batch_column Source code
read_OnDiskLongTable_block Source code
read_OnDiskLongTable_column Source code
read_object Source code
read_seqinfo_table Source code
referenceGenome Man page
referenceGenome,SNPlocs-method Man page
referenceGenome,XtraSNPlocs-method Man page
releaseDate,SNPlocs-method Man page
releaseDate,XtraSNPlocs-method Man page
releaseName,SNPlocs-method Man page
releaseName,XtraSNPlocs-method Man page
removeCommentLines Source code
remove_dirs Source code Source code
remove_file Source code Source code
replace_non_ACGTN_with_N Source code
rowids2rowidx Source code Source code Source code
rowidx2rowkeys Source code Source code
saveAsOnDiskLongTable_old Source code
saveObject Source code
saveRowidsForOnDiskLongTable_old Source code
save_object 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,BSgenomeViews-method Man page
seqnames,SNPlocs-method Man page
seqnames,XtraSNPlocs-method Man page
seqnames2batchidx Source code
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
snpid2alleles Man page
snpid2alleles,OldFashionSNPlocs-method Man page
snpid2alleles,SNPlocs-method Man page
snpid2alleles_OldFashionSNPlocs Source code
snpid2grange Man page
snpid2grange,OldFashionSNPlocs-method Man page
snpid2grange,SNPlocs-method Man page
snpid2grange_OldFashionSNPlocs Source code
snpid2loc Man page
snpid2loc,OldFashionSNPlocs-method Man page
snpid2loc,SNPlocs-method Man page
snpid2loc_OldFashionSNPlocs Source code
snpid2rowidx Source code
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
snpsById_ODLT_SNPlocs Source code
snpsById_OldFashionSNPlocs Source code
snpsByOverlaps Man page
snpsByOverlaps,ODLT_SNPlocs-method Man page
snpsByOverlaps,OldFashionSNPlocs-method Man page
snpsByOverlaps,SNPlocs-method Man page
snpsByOverlaps,XtraSNPlocs-method Man page
snpsByOverlaps_ODLT_SNPlocs Source code
snpsByOverlaps_OldFashionSNPlocs Source code
snpsBySeqname Man page
snpsBySeqname,ODLT_SNPlocs-method Man page
snpsBySeqname,OldFashionSNPlocs-method Man page
snpsBySeqname,SNPlocs-method Man page
snpsBySeqname,XtraSNPlocs-method Man page
snpsBySeqname_ODLT_SNPlocs Source code
snpsBySeqname_OldFashionSNPlocs Source code
sourceUrl Man page
sourceUrl,BSgenome-method Man page
species,XtraSNPlocs-method Man page
splitNameParts Source code
starfreeStrand Source code
start,BSgenomeViews-method Man page
stopOnAvailablePkg Source code
stopOnMoreThanOneAvailablePkg Source code
strand,BSgenomeViews-method Man page
subject,BSgenomeViews-method Man page
subsetTwobitFile Source code
toGRanges Source code
to_DataFrame Source code
uniqueLetters,BSgenomeViews-method Man page
unlist,BSgenomeViews-method Man page
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
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
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
Bioconductor/BSgenome documentation built on July 19, 2018, 8:17 p.m.