https://github.com/angelbee2018/jum
A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
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A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
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Fork of qqwang-berkeley/JUM
Created over 6 years ago
· Last pushed almost 7 years ago
https://github.com/angelbee2018/JUM/blob/master/
# The Junction Usage Model (JUM)
- JUM is a tool that offers a completely annotation-free approach to analyze alternative pre-mRNA splicing patterns that are specific to a tissue or sample of interest from RNA-seq datasets.
* Stable performance packages for V2.0.2:
* Complete manual for V2.0.2:
* For differential AS analysis among multiple experimental conditions see: https://github.com/qqwang-berkeley/JUM/wiki/6.-Running-JUM-for-differential-AS-analysis-among-multiple-experimental-conditions-(multiple-tissues,-patients,-time-series-experiments-etc.)
- JUM reports alternative splicing events in six categories: cassette exon, mutually exclusive exons, alternative 5' splice site, alternative 3' splice site, intron retention, Composite patterns
- JUM does not depend on any prior knowledge of a transcriptome annotation nor known libraries of AS events.
- The JUM method is published:
The simulated RNA-seq datasets and ground truth (true AS genes and non-AS genes) described in the paper are deposited in GEO with accession number GSE118193.
- Feel free to post any questions or comments on the Google group for JUM users:
* Legacy manual for V2.0 and V2.0.1:
* Legacy manual for V1.3.12:
Owner
- Login: angelbee2018
- Kind: user
- Repositories: 1
- Profile: https://github.com/angelbee2018