Package: BSgenomeForge 1.7.0

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_1.7.0.tar.gz
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BSgenomeForge.pdf |BSgenomeForge.html✨
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-1.7.0(bioc 3.21)BSgenomeForge-1.6.0(bioc 3.20)

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

6.30 score 4 stars 4 scripts 244 downloads 12 exports 51 dependencies

Last updated 2 months agofrom:b850d528a1. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	ERROR	Nov 29 2024
R-4.5-linux	ERROR	Nov 29 2024
R-4.4-win	ERROR	Nov 29 2024
R-4.4-mac	ERROR	Nov 29 2024
R-4.3-win	ERROR	Nov 29 2024
R-4.3-mac	ERROR	Nov 29 2024

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

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics 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

A quick introduction to the BSgenomeForge package

Atuhurira Kirabo Kakopo, Hervé Pagès

Rendered fromQuickBSgenomeForge.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Advanced BSgenomeForge usage

Rendered fromAdvancedBSgenomeForge.Rnwusingutils::Sweaveon Nov 29 2024.

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