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-any)BSgenomeForge_1.13.0.zip(r-4.6-any)BSgenomeForge_1.13.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
BSgenomeForge/json (API)

# 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)

infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package

6.57 score 5 stars 30 scripts 632 downloads 12 exports 44 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksWARNING193
linux-develERROR339
source / vignettesOK271
linux-releaseERROR344
macos-releaseERROR190
macos-oldrelERROR206
windows-develERROR189
windows-releaseERROR228
windows-oldrelERROR246
wasm-releaseOK148

Exports:downloadGenomicSequencesFromNCBIdownloadGenomicSequencesFromUCSCfastaTo2bitforgeBSgenomeDataPkgforgeBSgenomeDataPkgFromNCBIforgeBSgenomeDataPkgFromTwobitFileforgeBSgenomeDataPkgFromUCSCforgeMaskedBSgenomeDataPkgforgeMasksFilesforgeSeqFilesforgeSeqlengthsRdaFileforgeSeqlengthsRdsFile

Dependencies:askpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecigarillocodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4VectorsSeqinfosnowsysUCSC.utilsXMLXVectoryaml

A quick introduction to the BSgenomeForge package
Introduction | Installation | Basic usage | Using forgeBSgenomeDataPkgFromNCBI() | Using forgeBSgenomeDataPkgFromUCSC() | Final steps | sessionInfo()
Rendered fromQuickBSgenomeForge.Rmdusingknitr::rmarkdown

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

Advanced BSgenomeForge usage
Introduction | How to forge a BSgenome data package with bare sequences | How to forge a BSgenome data package with masked sequences | Session information
Rendered fromAdvancedBSgenomeForge.Rnwusingutils::Sweave

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

Readme and manuals

Help Manual

Help pageTopics
The BSgenomeForge packageBSgenomeForge-package BSgenomeForge
Advanced BSgenomeForge functionsAdvancedBSgenomeForge 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 NCBIdownloadGenomicSequencesFromNCBI
Download genomic sequences from UCSCdownloadGenomicSequencesFromUCSC
Convert files from FASTA to 2bitfastaTo2bit
Create a BSgenome data package from an NCBI assemblyforgeBSgenomeDataPkgFromNCBI
Create a BSgenome data package from a 2bit fileforgeBSgenomeDataPkgFromTwobitFile
Create a BSgenome data package from a UCSC genomeforgeBSgenomeDataPkgFromUCSC