branchpointer

This is the released version of branchpointer; for the devel version, see branchpointer.

Prediction of intronic splicing branchpoints

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DOI: 10.18129/B9.bioc.branchpointer

Bioconductor version: Release (3.22)

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 "4.5") 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

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GenomeAnnotation, GenomicVariation, MotifAnnotation, Software

Version 1.35.1

In Bioconductor since BioC 3.5 (R-3.4) (8.5 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, Seqinfo, IRanges, S4Vectors, data.table

System Requirements

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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

Windows Binary (x86_64) branchpointer_1.35.1.zip

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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