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

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

Bioconductor version: Development (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>

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


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

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.19.1
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 (>=
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
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
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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/
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