branchpointer

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see branchpointer.

Prediction of intronic splicing branchpoints


Bioconductor version: 3.7

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 "3.5") 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 PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GenomeAnnotation, GenomicVariation, MotifAnnotation, Software
Version 1.6.0
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
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_1.6.0.tar.gz
Windows Binary branchpointer_1.6.0.zip
Mac OS X 10.11 (El Capitan) branchpointer_1.6.0.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
Old Source Packages for BioC 3.7 Source Archive