JunctionSeq

Differential Usage of Exons and Splice Junctions

View the Project on GitHub Stephen Hartley

> v0.99.8 (Revised Thu Jan 21 13:51:03 EST 2016)

JunctionSeq is an R package for detection and visualization of differential usage of exons and splice junctions in High-Throughput, Next-Generation RNA-Seq datasets. The methodology is heavily based on the DEXSeq bioconductor package, originally proposed by Anders, Reyes, and Huber. More information is available on the JunctionSeq GitHub Pages.

The core advantage of JunctionSeq over other similar tools is that it provides a powerful automated tools for generating readable and interpretable plots and tables to facilitate the interpretation of the results. An example results report is available here. An example set of browser tracks from this same dataset is available here, which uses this trackhub.

Issues, bug reports, or feature requests can be posted to the github issues page. The developers can be contacted at JunctionSeq-Contact (at) list.nih.gov.

Note: the current version of JunctionSeq is ONLY compatible with Bioconductor 3.2 or higher.

JunctionSeq has been pre-accepted into Bioconductor, and will probably be included in the next Bioconductor release. Even after JunctionSeq is added to Bioconductor we will continue to update and maintain this page, as this page provides additional online help and documentation.

HELP AND DOCUMENTATION:

The JunctionSeq user manual: An introduction to differential usage analysis with JunctionSeq.
The online reference documentation: The complete JunctionSeq R documentation.
A comprehensive walkthrough: describes the entire analysis pipeline from aligned reads through analysis. This includes analysis with other tools such as DESeq2, edgeR, and DEXSeq, as well as the creation of plots and browser tracks.
Example dataset: used with the walkthrough so you can follow along (~280mb download). The example bam files are separate (~1gb download).
An example results report: An example of the plots and html files produced by JunctionSeq (created using the example dataset).
An example set of browser tracks from this same dataset is available here. The trackhub used to generate this session can be found here
Frequently Asked Questions: If you still have questions, check here.

Note: The example dataset and results are for testing and demonstration purposes only. The samples and annotation have been heavily modified and down-sampled both to test artificial edge cases and to provide smaller and more portable testing files. The results should not be taken as an indication of any biological phenomenon.

For help with individual R functions in the R utility, use the R command:

> help(functionname);

For a full listing of all help topics for the R utility, use the R command:

> help(package="JunctionSeq");

CITING JUNCTIONSEQ:

You can currently cite the JunctionSeq methods paper preprint as:

Hartley SW, Mullikin JC. Detection and Visualization of Differential Exon and Splice Junction Usage in RNA-Seq Data with JunctionSeq. arXiv preprint arXiv:1512.06038. 2015 Dec 18.

INSTALLATION:

JunctionSeq can be installed automatically in R using the command:

> source("http://hartleys.github.io/JunctionSeq/install/JS.install.R");
> JS.install();

See the FAQ for advanced installation options.

The splice, gene, and exon read-counts required by JunctionSeq can be created using the QoRTs software package, available here.

EXAMPLE DATA:

Another example dataset, used in the vignette, is packaged as an R package, and can be installed with the command:

> install.packages("http://hartleys.github.io/JunctionSeq/install/JctSeqData_LATEST.tar.gz", 
                  repos = NULL, 
                  type="source")

LEGAL:

This software package is licensed under the GNU-GPL v3:

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Portions of this software are "United States Government Work" under the terms of the United States Copyright Act.
It was written as part of the authors' official duties for the United States Government and thus those portions cannot be copyrighted. Those portions of this software are freely available to the public for use without a copyright notice.
Restrictions cannot be placed on its present or future use.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose.