SUPPA protocols

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description
SUPPA computational protocol

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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Additional information


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

Publications for SUPPA

SUPPA IN pipeline

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

[…] differential expression between wt and ko md cell lines, with 146 genes up-regulated, and 142 genes down-regulated (table s2). we then assessed splicing changes in the rbm10 ko cell lines using the suppa tool,32 which calculates the psi (“percentage spliced in”) value for each splicing event extracted from the annotation of the mm10 mouse genome. we defined a list of differential splicing […]

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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