branchpointer
Prediction of intronic splicing branchpoints
Bioconductor version: Release (3.19)
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 (from within R, enter
citation("branchpointer")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.30.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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, GenomeInfoDb, 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_1.30.0.tar.gz |
| Windows Binary (x86_64) | branchpointer_1.30.0.zip (64-bit only) |
| macOS Binary (x86_64) | branchpointer_1.30.0.tgz |
| macOS Binary (arm64) | branchpointer_1.30.0.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 |