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branchpointer

This is the development version of branchpointer; for the stable release version, see branchpointer.

Prediction of intronic splicing branchpoints


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
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 PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GenomeAnnotation, GenomicVariation, MotifAnnotation, Software
Version 1.29.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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Suggests knitr, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package branchpointer_1.29.0.tar.gz
Windows Binary branchpointer_1.29.0.zip
macOS Binary (x86_64) branchpointer_1.29.0.tgz
macOS Binary (arm64) branchpointer_1.29.0.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