branchpointer

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see branchpointer.

Prediction of intronic splicing branchpoints

Bioconductor version: 3.6

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 "3.4") 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 PDF R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GenomeAnnotation, GenomicVariation, MotifAnnotation, Software

Version 1.4.0

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_1.4.0.tar.gz

Windows Binary branchpointer_1.4.0.zip

Mac OS X 10.11 (El Capitan) branchpointer_1.4.0.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/

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Old Source Packages for BioC 3.6 Source Archive