JunctionSeq

DOI: 10.18129/B9.bioc.JunctionSeq    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last 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: 3.12

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

PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.3 (R-3.3) (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
Windows Binary
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