Splicing Express protocols

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chevron_left Alternative splicing events identification Transcriptome annotation Alternative splicing visualization chevron_right
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Splicing Express specifications


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



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  • person_outline Sandro de Souza <>

Publication for Splicing Express

Splicing Express in pipeline

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

[…] as event, while intron retention is the rarest one, i.e. they comprise 36.7% and 12.2% of all gm as events, respectively (additional fileĀ : table s4). similar results were obtained with the splicing express software [] (additional fileĀ : table s4), i.e. exon skipping was the most prevalent as event (41.1%) and intron retention the least favoured one (12.7%)., we used two different […]

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Splicing Express in publications

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

[…] estimate of the log2fc is divided by its standard error, generating a z-statistic that can be compared to a standard normal distribution []., to classify splicing events with the suppa [] and splicing express [] softwares, genome bam files were generated with the star software [], by using the same parameters described above. these bam files were employed to assemble transcripts […]

PMCID: 5582454
PMID: 28912681
DOI: 10.3389/fnmol.2017.00275

[…] (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 […]

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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.

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