JunctionSeq

DOI: 10.18129/B9.bioc.JunctionSeq    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see JunctionSeq.

JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

Bioconductor version: 3.11

A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.

Author: Stephen Hartley [aut, cre] (PhD), Simon Anders [cph], Alejandro Reyes [cph]

Maintainer: Stephen Hartley <JunctionSeq-contact at list.nih.gov>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("JunctionSeq")

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("JunctionSeq")

 

PDF		JunctionSeq Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.17.0
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
License	file LICENSE
Depends	R (>= 3.2.2), methods, SummarizedExperiment(>= 0.2.0), Rcpp (>= 0.11.0), RcppArmadillo (>= 0.3.4.4)
Imports	DESeq2(>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase(>= 2.30.0), locfit, BiocGenerics(>= 0.7.5), BiocParallel, genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges
LinkingTo	Rcpp, RcppArmadillo
Suggests	MASS, knitr, JctSeqData, BiocStyle
SystemRequirements
Enhances	Cairo, pryr
URL	http://hartleys.github.io/JunctionSeq/index.html
BugReports	https://github.com/hartleys/JunctionSeq/issues
Depends On Me
Imports Me	PathwaySplice
Suggests Me	JctSeqData, snapcount
Links To Me
Build Report

Package Archives

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

Source Package	JunctionSeq_1.17.0.tar.gz
Windows Binary	JunctionSeq_1.17.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/JunctionSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/JunctionSeq
Package Short Url	https://bioconductor.org/packages/JunctionSeq/
Package Downloads Report	Download Stats