JunctionSeq

This package is for version 3.8 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

DOI: 10.18129/B9.bioc.JunctionSeq

Bioconductor version: 3.8

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 "3.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software

Version 1.12.1

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

Suggests MASS, knitr, JctSeqData, BiocStyle

Linking To Rcpp, RcppArmadillo

Enhances Cairo, pryr

Depends On Me

Imports Me PathwaySplice

Suggests Me JctSeqData

Links To Me

Build Report Build Report

Package Archives

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

Source Package JunctionSeq_1.12.1.tar.gz

Windows Binary JunctionSeq_1.12.1.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) JunctionSeq_1.12.1.tgz

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 3.8 Source Archive