JunctionSeq

DOI: 10.18129/B9.bioc.JunctionSeq    

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")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.0
In Bioconductor since BioC 3.3 (R-3.3) (4 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

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