Package: BSgenomeForge 1.13.0

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_1.13.0.tar.gz
BSgenomeForge_1.13.0.zip(r-4.7)BSgenomeForge_1.13.0.zip(r-4.6)BSgenomeForge_1.13.0.zip(r-4.5)
BSgenomeForge_1.13.0.tgz(r-4.6-any)BSgenomeForge_1.13.0.tgz(r-4.5-any)
BSgenomeForge_1.13.0.tar.gz(r-4.7-any)BSgenomeForge_1.13.0.tar.gz(r-4.6-any)
BSgenomeForge_1.13.0.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.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

6.54 score 5 stars 20 scripts 486 downloads 12 exports 52 dependencies

Last updated from:34fd2f466a. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	230
linux-devel-x86_64	ERROR	428
source / vignettes	OK	363
linux-release-x86_64	ERROR	379
macos-release-arm64	ERROR	240
macos-oldrel-arm64	ERROR	179
windows-devel	ERROR	299
windows-release	ERROR	312
windows-oldrel	ERROR	278
wasm-release	OK	181

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

Dependencies:abind askpass BH Biobase BiocBaseUtils 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 May 28 2026.

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

Advanced BSgenomeForge usage

Rendered fromAdvancedBSgenomeForge.Rnwusingutils::Sweaveon May 28 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