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SUPPA specifications

Information


Unique identifier OMICS_05583
Name SUPPA
Alternative name SUPPA2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format GTF + TEF
Operating system Unix/Linux
Programming languages Python, R
License MIT License
Computer skills Advanced
Version 2.1
Stability Stable
Requirements
SciPy, NumPy, Pandas, statsmodels, scikit-learn
Source code URL https://codeload.github.com/comprna/SUPPA/tar.gz/v2.1
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Eduardo Eyras

Additional information


https://github.com/comprna/SUPPA/wiki

Publications for SUPPA

SUPPA citations

 (10)
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

[…] event categories in the porcine skeletal muscle, the sets of genes identified by these two softwares as yielding alternative transcripts were quite different. The proportions of genes overlapping the SUPPA and Splicing Express data sets classified according to the type of AS event were: exon skipping = 27%, alternative 5′ =24%, 3′ splice sites = 20% and intron retention = 14%. Though we do not hav […]

library_books

Impact of Prefrontal Theta Burst Stimulation on Clinical Neuropsychological Tasks

2017
Front Neurosci
PMCID: 5563370
PMID: 28867993
DOI: 10.3389/fnins.2017.00462

[…] ang et al., , , ). Stimulus intensity was set at 80% of the individually estimated aMT following the common practice and the published international safety guidelines (Huang et al., ; Rossi et al., ; Suppa et al., ). Precise identification of left dlPFC target site, TMS coil positioning, and adequate targeting during stimulation was controlled with the above-mentioned frameless stereotaxic system […]

library_books

Genome Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis

2017
Front Microbiol
PMCID: 5440512
PMID: 28588571
DOI: 10.3389/fmicb.2017.00929

[…] losus (; ) and E. multilocularis () by HISAT (), and then assembled with StringTie () to construct unique transcript sequences, using the parameters: -g -b -u -o. AS events in a gene were detected by SUPPA (). Cuffquant () was used to quantify the expression of genes and transcripts, and the raw expression values were normalized by Cuffnorm. The expression values were calculated for each sample ba […]

library_books

Trends and challenges in computational RNA biology

2016
Genome Biol
PMCID: 5141647
PMID: 27927225
DOI: 10.1186/s13059-016-1117-7

[…] ose alternative exclusion is associated with the autism phenotype. Isoform quantification methods were discussed by Eduardo Eyras (University of Pompeu Fabra, Barcelona, Spain), who explained how the SUPPA method achieves high computational performance by decoupling read mapping from transcript annotation. Methodologies for isoform quantification from time series RNA-seq data using the DICEseq met […]

library_books

The RNA binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

2016
RNA Biol
PMCID: 5270529
PMID: 27763814
DOI: 10.1080/15476286.2016.1247148

[…] q. We calculated the Euclidean distances among samples and used heatmap2 function of the gplot package to visualize the sample clustering. The Genome-wide analyses of pre-mRNA splicing was done using SUPPA. This method generated a list of splicing events from the mm10 annotation and then used the transcript quantification from Sailfish to calculate the PSI value for each splicing event (or transcr […]

library_books

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non coding genes

2016
eLife
PMCID: 5053804
PMID: 27623010
DOI: 10.7554/eLife.15614.024

[…] Using a previously established pipeline for analysis of alternative splicing events, SUPPA (see Materials and methods), we identified 7564 alternative splicing events affecting 3599 genes (). An alternative first exon was most common, accounting for the majority of alternative splicin […]

Citations

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SUPPA institution(s)
Pompeu Fabra University, Barcelona, Spain; University of Dundee, Invergowrie, Dundee, UK; Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, UK; ICREA, Barcelona, Spain
SUPPA funding source(s)
Supported by the MINECO, FEDER (BIO2014-52566-R), AGAUR (SGR2014-1121) and Breast Cancer Now (2014NovPR355).

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