Package: BSgenomeForge 1.12.0

Hervé Pagès

BSgenomeForge: Forge your own BSgenome data package

A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.

Authors:Hervé Pagès [aut, cre], Atuhurira Kirabo Kakopo [aut], Emmanuel Chigozie Elendu [ctb], Prisca Chidimma Maduka [ctb]

BSgenomeForge_1.12.0.tar.gz
BSgenomeForge_1.12.0.zip(r-4.7)BSgenomeForge_1.12.0.zip(r-4.6)BSgenomeForge_1.12.0.zip(r-4.5)
BSgenomeForge_1.12.0.tgz(r-4.6-any)BSgenomeForge_1.12.0.tgz(r-4.5-any)
BSgenomeForge_1.12.0.tar.gz(r-4.7-any)BSgenomeForge_1.12.0.tar.gz(r-4.6-any)
BSgenomeForge_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BSgenomeForge/json (API)
NEWS

# Install 'BSgenomeForge' in R:

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

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

On BioConductor:BSgenomeForge-1.13.0(bioc 3.24)BSgenomeForge-1.12.0(bioc 3.23)

infrastructure datarepresentation genomeassembly annotation genomeannotation sequencing alignment dataimport sequencematching bioconductor-package core-package

6.60 score 5 stars 23 scripts 458 downloads 12 exports 51 dependencies

Last updated from:d920cea8b5 (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	280
linux-devel-x86_64	ERROR	470
source / vignettes	OK	337
linux-release-x86_64	ERROR	459
macos-release-arm64	ERROR	242
macos-oldrel-arm64	ERROR	217
windows-devel	ERROR	329
windows-release	ERROR	302
windows-oldrel	ERROR	308
wasm-release	OK	201

Exports:downloadGenomicSequencesFromNCBI downloadGenomicSequencesFromUCSC fastaTo2bit forgeBSgenomeDataPkg forgeBSgenomeDataPkgFromNCBI forgeBSgenomeDataPkgFromTwobitFile forgeBSgenomeDataPkgFromUCSC forgeMaskedBSgenomeDataPkg forgeMasksFiles forgeSeqFiles forgeSeqlengthsRdaFile forgeSeqlengthsRdsFile

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

A quick introduction to the BSgenomeForge package

Atuhurira Kirabo Kakopo, Hervé Pagès

Rendered fromQuickBSgenomeForge.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2024-04-08
Started: 2024-03-31

Advanced BSgenomeForge usage

Rendered fromAdvancedBSgenomeForge.Rnwusingutils::Sweaveon Jun 08 2026.

Last update: 2024-03-31
Started: 2024-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The BSgenomeForge package	BSgenomeForge-package BSgenomeForge
Advanced BSgenomeForge functions	AdvancedBSgenomeForge BSgenomeDataPkgSeed BSgenomeDataPkgSeed-class class:BSgenomeDataPkgSeed forgeBSgenomeDataPkg forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method forgeBSgenomeDataPkg,character-method forgeBSgenomeDataPkg,list-method forgeMaskedBSgenomeDataPkg forgeMaskedBSgenomeDataPkg,character-method forgeMaskedBSgenomeDataPkg,list-method forgeMaskedBSgenomeDataPkg,MaskedBSgenomeDataPkgSeed-method forgeMasksFiles forgeSeqFiles forgeSeqlengthsRdaFile forgeSeqlengthsRdsFile
Download genomic sequences from NCBI	downloadGenomicSequencesFromNCBI
Download genomic sequences from UCSC	downloadGenomicSequencesFromUCSC
Convert files from FASTA to 2bit	fastaTo2bit
Create a BSgenome data package from an NCBI assembly	forgeBSgenomeDataPkgFromNCBI
Create a BSgenome data package from a 2bit file	forgeBSgenomeDataPkgFromTwobitFile
Create a BSgenome data package from a UCSC genome	forgeBSgenomeDataPkgFromUCSC