branchpointer

DOI: 10.18129/B9.bioc.branchpointer    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see branchpointer.

Prediction of intronic splicing branchpoints

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Using Branchpointer for annotation of intronic human splicing branchpoints
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GenomeAnnotation, GenomicVariation, MotifAnnotation, Software
Version	1.10.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 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
LinkingTo
Suggests	knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	branchpointer_1.10.0.tar.gz
Windows Binary	branchpointer_1.10.0.zip
Mac OS X 10.11 (El Capitan)	branchpointer_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/branchpointer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/branchpointer
Package Short Url	https://bioconductor.org/packages/branchpointer/
Package Downloads Report	Download Stats