branchpointer

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Prediction of intronic splicing branchpoints

Bioconductor version: Development (3.24)

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")):

Beth Signal. branchpointer: Prediction of intronic splicing branchpoints. doi:10.18129/B9.bioc.branchpointer, R package version 1.39.0, https://bioconductor.org/packages/branchpointer.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomeAnnotation, GenomicVariation, MotifAnnotation, Software
Version	1.39.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 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
URL

Suggests	knitr, BiocStyle
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	branchpointer_1.39.0.tar.gz
Windows Binary (x86_64)	branchpointer_1.39.0.zip
macOS Binary (big-sur-x86_64)	branchpointer_1.39.0.tgz
macOS Binary (sonoma-arm64)	branchpointer_1.39.0.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