BSgenomeForge
This is the development version of BSgenomeForge; for the stable release version, see BSgenomeForge.
Forge your own BSgenome data package
Bioconductor version: Development (3.24)
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.
Author: Hervé Pagès [aut, cre], Atuhurira Kirabo Kakopo [aut], Emmanuel Chigozie Elendu [ctb], Prisca Chidimma Maduka [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("BSgenomeForge")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BSgenomeForge")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BSgenomeForge")| A quick introduction to the BSgenomeForge package | HTML | R Script |
| Advanced BSgenomeForge usage | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, DataImport, DataRepresentation, GenomeAnnotation, GenomeAssembly, Infrastructure, SequenceMatching, Sequencing, Software |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), methods, BiocGenerics, IRanges, Seqinfo, GenomeInfoDb(>= 1.45.5), Biostrings(>= 2.77.2), BSgenome(>= 1.77.1) |
| Imports | utils, stats, Biobase, S4Vectors(>= 0.47.6), GenomicRanges(>= 1.61.1), BiocIO, rtracklayer(>= 1.69.1) |
| System Requirements | |
| URL | https://bioconductor.org/packages/BSgenomeForge |
| Bug Reports | https://github.com/Bioconductor/BSgenomeForge/issues |
See More
| Suggests | GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | BSgenome, TmCalculator |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BSgenomeForge_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | BSgenomeForge_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | BSgenomeForge_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BSgenomeForge |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BSgenomeForge |
| Bioc Package Browser | https://code.bioconductor.org/browse/BSgenomeForge/ |
| Package Short Url | https://bioconductor.org/packages/BSgenomeForge/ |
| Package Downloads Report | Download Stats |