BREW3R.r
This is the released version of BREW3R.r; for the devel version, see BREW3R.r.
R package associated to BREW3R
Bioconductor version: Release (3.23)
This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.
Author: Lucille Lopez-Delisle [aut, cre]
Maintainer: Lucille Lopez-Delisle <lucille.delisle at epfl.ch>
citation("BREW3R.r")):
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")
BiocManager::install("BREW3R.r")
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("BREW3R.r")| BREW3R.r | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GenomeAnnotation, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | GenomicRanges, methods, rlang, S4Vectors, utils |
| System Requirements | |
| URL | https://github.com/lldelisle/BREW3R.r |
| Bug Reports | https://github.com/lldelisle/BREW3R.r/issues/ |
See More
| Suggests | testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BREW3R.r_1.8.0.tar.gz |
| Windows Binary (x86_64) | BREW3R.r_1.8.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BREW3R.r_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | BREW3R.r_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BREW3R.r |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BREW3R.r |
| Bioc Package Browser | https://code.bioconductor.org/browse/BREW3R.r/ |
| Package Short Url | https://bioconductor.org/packages/BREW3R.r/ |
| Package Downloads Report | Download Stats |