Package: BSgenome 1.75.0

Hervé Pagès

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

Infrastructure shared by all the Biostrings-based genome data packages.

Authors:Hervé Pagès [aut, cre]

BSgenome_1.75.0.tar.gz
BSgenome_1.75.0.zip(r-4.5)BSgenome_1.75.0.zip(r-4.4)BSgenome_1.75.0.zip(r-4.3)
BSgenome_1.75.0.tgz(r-4.4-any)BSgenome_1.75.0.tgz(r-4.3-any)
BSgenome_1.75.0.tar.gz(r-4.5-noble)BSgenome_1.75.0.tar.gz(r-4.4-noble)
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BSgenome.pdf |BSgenome.html✨
BSgenome/json (API)
NEWS

# Install 'BSgenome' in R:

install.packages('BSgenome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/bsgenome/issues

On BioConductor:BSgenome-1.73.1(bioc 3.20)BSgenome-1.72.0(bioc 3.19)

genetics infrastructure datarepresentation sequencematching annotation snp bioconductor-package core-package

13.17 score 9 stars 268 packages 1.1k scripts 25k downloads 91 exports 49 dependencies

Last updated 23 days agofrom:c53bfc0656. Checks:OK: 1 WARNING: 5 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 30 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	ERROR	Oct 30 2024

Exports:alphabetFrequency as.data.frame as.data.frame.BSgenomeViews as.list available.genomes available.SNPs batchsizes blocksizes breakpoints bsapply BSgenome BSgenomeViews coerce commonName compatibleGenomes consensusMatrix consensusString countPWM elementNROWS end export extractAt forgeBSgenomeDataPkg forgeMaskedBSgenomeDataPkg forgeMasksFiles forgeSeqFiles forgeSeqlengthsRdaFile forgeSeqlengthsRdsFile getBatchesByOverlapsFromOnDiskLongTable getBatchesBySeqnameFromOnDiskLongTable getBatchesFromOnDiskLongTable getBatchesFromOnDiskLongTable_old getBSgenome getRowsByIdFromOnDiskLongTable getRowsByIndexFromOnDiskLongTable_old getRowsFromOnDiskLongTable getSeq granges hasOnlyBaseLetters inferRefAndAltAlleles injectSNPs installed.genomes installed.SNPs letterFrequency MaskedBSgenome masknames matchPWM mseqnames nchar newSNPlocs newXtraSNPlocs nucleotideFrequencyAt oligonucleotideFrequency OnDiskLongTable OnDiskLongTable_old organism provider providerVersion ranges referenceGenome releaseDate releaseName saveAsOnDiskLongTable_old saveRowidsForOnDiskLongTable_old score seqinfo seqinfo<-seqnames seqnames<-seqtype show snpcount snplocs SNPlocs_pkgname snpsById snpsByOverlaps snpsBySeqname sourceUrl spatialIndex start strand subject uniqueLetters vcountPattern Views vmatchPattern width writeBSgenomeToFasta writeBSgenomeToTwobit writeOnDiskLongTable writeOnDiskLongTableRowids

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XML XVector yaml zlibbioc

Efficient genome searching with Biostrings and the BSgenome data packages

Rendered fromGenomeSearching.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2024-02-07
Started: 2013-11-01

How to forge a BSgenome data package

Rendered fromBSgenomeForge.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2024-03-31
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
[Moved to BSgenomeForge] Tools to forge a BSgenome data package	AdvancedBSgenomeForge forgeBSgenomeDataPkg forgeMaskedBSgenomeDataPkg forgeMasksFiles forgeSeqFiles forgeSeqlengthsRdaFile forgeSeqlengthsRdsFile
Find available/installed genomes	available.genomes getBSgenome installed.genomes
bsapply	bsapply
BSgenome objects	$,BSgenome-method as.list,BSgenome-method BSgenome BSgenome-class bsgenomeName,BSgenome-method class:BSgenome coerce,BSgenome,GenomeDescription-method commonName,BSgenome-method length,BSgenome-method masknames masknames,BSgenome-method masknames,MaskedBSgenome-method mseqnames mseqnames,BSgenome-method names,BSgenome-method organism,BSgenome-method provider,BSgenome-method providerVersion,BSgenome-method releaseDate,BSgenome-method seqinfo,BSgenome-method seqinfo<-,BSgenome-method seqnames,BSgenome-method seqnames<-,BSgenome-method show,BSgenome-method sourceUrl sourceUrl,BSgenome-method [[,BSgenome-method
BSgenome utilities	BSgenome-utils countPWM,BSgenome-method matchPWM,BSgenome-method vcountPattern,BSgenome-method vcountPDict,BSgenome-method vmatchPattern,BSgenome-method vmatchPDict,BSgenome-method
BSgenomeViews objects	alphabetFrequency,BSgenomeViews-method as.character,BSgenomeViews-method as.data.frame,BSgenomeViews-method BSgenomeViews BSgenomeViews-class class:BSgenomeViews coerce,BSgenomeViews,DNAStringSet-method coerce,BSgenomeViews,XStringSet-method consensusMatrix,BSgenomeViews-method consensusString,BSgenomeViews-method elementNROWS,BSgenomeViews-method end,BSgenomeViews-method extractROWS,BSgenomeViews-method getListElement,BSgenomeViews-method granges,BSgenomeViews-method hasOnlyBaseLetters,BSgenomeViews-method length,BSgenomeViews-method letterFrequency,BSgenomeViews-method names,BSgenomeViews-method nchar,BSgenomeViews-method nucleotideFrequencyAt,BSgenomeViews-method oligonucleotideFrequency,BSgenomeViews-method ranges,BSgenomeViews-method seqinfo,BSgenomeViews-method seqnames,BSgenomeViews-method seqtype,BSgenomeViews-method show,BSgenomeViews-method start,BSgenomeViews-method strand,BSgenomeViews-method subject,BSgenomeViews-method uniqueLetters,BSgenomeViews-method unlist,BSgenomeViews-method Views,BSgenome-method width,BSgenomeViews-method
Class "BSParams"	BSParams BSParams-class class:BSParams
Export a BSgenome object as a FASTA or twoBit file	export,BSgenome,FastaFile,ANY-method export,BSgenome,TwoBitFile,ANY-method export-methods writeBSgenomeToFasta writeBSgenomeToTwobit
getSeq methods for BSgenome and XStringSet objects	getSeq getSeq,BSgenome-method getSeq,XStringSet-method [,XStringSet,GenomicRanges-method [,XStringSet,GRangesList-method
SNP injection	available.SNPs class:InjectSNPsHandler injectSNPs injectSNPs,BSgenome-method InjectSNPsHandler InjectSNPsHandler-class installed.SNPs snpcount,BSgenome-method snpcount,InjectSNPsHandler-method snplocs,BSgenome-method snplocs,InjectSNPsHandler-method SNPlocs_pkgname SNPlocs_pkgname,BSgenome-method SNPlocs_pkgname,InjectSNPsHandler-method
SNPlocs objects	class:ODLT_SNPlocs class:OldFashionSNPlocs class:SNPlocs commonName,SNPlocs-method compatibleGenomes compatibleGenomes,SNPlocs-method inferRefAndAltAlleles newSNPlocs new_ODLT_SNPlocs ODLT_SNPlocs ODLT_SNPlocs-class OldFashionSNPlocs OldFashionSNPlocs-class organism,SNPlocs-method provider,SNPlocs-method providerVersion,SNPlocs-method referenceGenome referenceGenome,SNPlocs-method releaseDate,SNPlocs-method releaseName releaseName,SNPlocs-method seqinfo,SNPlocs-method seqnames,SNPlocs-method show,SNPlocs-method snpcount snpcount,ODLT_SNPlocs-method snpcount,OldFashionSNPlocs-method snpcount,SNPlocs-method SNPlocs snplocs snplocs,ODLT_SNPlocs-method snplocs,OldFashionSNPlocs-method snplocs,SNPlocs-method SNPlocs-class snpsById snpsById,ODLT_SNPlocs-method snpsById,OldFashionSNPlocs-method snpsById,SNPlocs-method snpsByOverlaps snpsByOverlaps,ODLT_SNPlocs-method snpsByOverlaps,OldFashionSNPlocs-method snpsByOverlaps,SNPlocs-method snpsBySeqname snpsBySeqname,ODLT_SNPlocs-method snpsBySeqname,OldFashionSNPlocs-method snpsBySeqname,SNPlocs-method
XtraSNPlocs objects	class:XtraSNPlocs colnames,XtraSNPlocs-method commonName,XtraSNPlocs-method dim,XtraSNPlocs-method newXtraSNPlocs organism,XtraSNPlocs-method provider,XtraSNPlocs-method providerVersion,XtraSNPlocs-method referenceGenome,XtraSNPlocs-method releaseDate,XtraSNPlocs-method releaseName,XtraSNPlocs-method seqinfo,XtraSNPlocs-method seqnames,XtraSNPlocs-method show,XtraSNPlocs-method snpcount,XtraSNPlocs-method snpsById,XtraSNPlocs-method snpsByOverlaps,XtraSNPlocs-method snpsBySeqname,XtraSNPlocs-method species,XtraSNPlocs-method XtraSNPlocs XtraSNPlocs-class