Protocols

Splicing Express specifications

Information


Unique identifier OMICS_18041
Name Splicing Express
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Requires GTF files
Input format GTF
Output data Expression graphics
Output format HTML
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

Download


download.png
bitbucket.png

Versioning


No version available

Maintainer


  • person_outline Sandro de Souza

Publication for Splicing Express

Splicing Express citations

 (2)
library_books

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

2018
BMC Genomics
PMCID: 5813380
PMID: 29444639
DOI: 10.1186/s12864-018-4515-2

[…] clear sequestration and turnover of intron-retention transcripts have been involved in the downregulation of genes in tissues where they do not have a relevant physiological role []. Though SUPPA and Splicing Express yielded consistent results about the relative importance of distinct AS event categories in the porcine skeletal muscle, the sets of genes identified by these two softwares as yieldin […]

call_split

Divergence in Morris Water Maze Based Cognitive Performance under Chronic Stress Is Associated with the Hippocampal Whole Transcriptomic Modification in Mice

2017
PMCID: 5582454
PMID: 28912681
DOI: 10.3389/fnmol.2017.00275
call_split See protocol

[…] Base (Gene Only) and inclusion of both direct and indirect relationships. The analysis used Fisher's Exact Test to calculate p-values.Alternative splicing events (ASE) were identified by the software Splicing Express (Kroll et al., ). Briefly, All GTF files created by Cufflinks (Roberts et al., ) were inserted with the mouse genome reference sequence (mm10) to run the software Splicing Express tha […]

Splicing Express institution(s)
Institute of Bioinformatics and Biotechnology, Natal, Rio Grande do Norte, Brazil; Brain Institute, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
Splicing Express funding source(s)
This work was supported by CNPq: 501891/2013-7, 483775/2012-6; CAPES: edital 051/2013; NIH: D43TW007015, U54HL108460.

Splicing Express reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Splicing Express