JunctionSeq

This package is for version 3.11 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: 3.11

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>

Citation (from within R, enter citation("JunctionSeq")):

Installation

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


if (!require("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")
JunctionSeq Vignette PDF
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.17.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL http://hartleys.github.io/JunctionSeq/index.html
Bug Reports https://github.com/hartleys/JunctionSeq/issues
See More
Suggests MASS, knitr, JctSeqData, BiocStyle
Linking To Rcpp, RcppArmadillo
Enhances Cairo, pryr
Depends On Me
Imports Me PathwaySplice
Suggests Me JctSeqData, snapcount
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/JunctionSeq/
Package Short Url https://bioconductor.org/packages/JunctionSeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive