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 |
.copyTwobitFile | 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 |
.forge.AGAPSmask | Source code |
.forge.AMBmask | Source code |
.forge.RMmask | Source code |
.forge.TRFmask | Source code |
.forgeFastaRzFileFromFastaFiles | Source code |
.forgeMasksFile | Source code |
.forgeRdaSeqFile | Source code |
.forgeRdsSeqFile | Source code |
.forgeTwobitFileFromFastaFiles | 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 |
.getMasksObjname | 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_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 |
.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_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 |
.readSeedFile | 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 |
.removeCommentLines | Source code |
.remove_dirs | Source code Source code |
.remove_file | Source code Source code |
.replace_non_ACGTN_with_N | Source code |
.reverseComplement_PDict | Source code |
.rowids2rowidx | Source code Source code |
.rowidx2rowkeys | Source code Source code |
.saveObjectToRdaFile | Source code |
.saveObjectToRdsFile | Source code |
.save_object | Source code |
.seqnames2batchidx | Source code |
.set_BSgenome_seqinfo | 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 |
.sortUCSCTwobitFile | Source code |
.splitNameParts | Source code |
.starfreeStrand | Source code |
.stopOnAvailablePkg | Source code |
.stopOnMoreThanOneAvailablePkg | Source code |
.subsetTwobitFile | 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 |
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 |
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 |
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,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 |
forgeBSgenomeDataPkg | Man page |
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method | Man page |
forgeBSgenomeDataPkg,character-method | Man page |
forgeBSgenomeDataPkg,list-method | Man page |
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 |
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_data_annotation_contrib_url | 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 |
makeS4FromList | 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.dcf2 | Source code |
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,BSgenome-method | 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 |
snpid2alleles | Man page |
snpid2alleles,OldFashionSNPlocs-method | Man page |
snpid2alleles,SNPlocs-method | Man page |
snpid2grange | Man page |
snpid2grange,OldFashionSNPlocs-method | Man page |
snpid2grange,SNPlocs-method | Man page |
snpid2loc | Man page |
snpid2loc,OldFashionSNPlocs-method | Man page |
snpid2loc,SNPlocs-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 |
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