branchpointer
This is the development version of branchpointer; for the stable release version, see branchpointer.
Prediction of intronic splicing branchpoints
Bioconductor version: Development (3.24)
Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.
Author: Beth Signal
Maintainer: Beth Signal <b.signal at garvan.org.au>
citation("branchpointer")):
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("branchpointer")
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("branchpointer")| Using Branchpointer for annotation of intronic human splicing branchpoints | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GenomeAnnotation, GenomicVariation, MotifAnnotation, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | caret, R (>= 3.4) |
| Imports | plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, Seqinfo, IRanges, S4Vectors, data.table |
| System Requirements | |
| URL |
See More
| Suggests | knitr, BiocStyle |
| 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 | branchpointer_1.39.0.tar.gz |
| Windows Binary (x86_64) | branchpointer_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | branchpointer_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | branchpointer_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/branchpointer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/branchpointer |
| Bioc Package Browser | https://code.bioconductor.org/browse/branchpointer/ |
| Package Short Url | https://bioconductor.org/packages/branchpointer/ |
| Package Downloads Report | Download Stats |