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Citations per year

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Popular tool citations

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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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Additional information


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

Publications for SUPPA

SUPPA in pipelines

 (4)
2018
PMCID: 5813380
PMID: 29444639
DOI: 10.1186/s12864-018-4515-2

[…] file : table s3). interestingly, 93% of the genes identified by star/rsem/deseq2 as displaying alternative transcripts were also detected with clc bio. analysis of transcriptomic data with the suppa software [] evidenced that exon skipping is the most prevalent as event, while intron retention is the rarest one, i.e. they comprise 36.7% and 12.2% of all gm as events, respectively […]

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

[…] (; ) 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 […]

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, 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 events […]

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

[…] 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 […]


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SUPPA in publications

 (43)
PMCID: 5884878
PMID: 29651241
DOI: 10.3389/fnhum.2018.00123

[…] of intra- and inter-individual variability between protocols and across each measurement time point. human responses to nibs are known to be highly variable (ridding and ziemann, ; hamada et al., ; suppa et al., ). in one of the largest single studies to date (n = 57), hamada et al. () showed that a single application of ctbs, or intermittent tbs (itbs) to the left-m1 resulted in highly […]

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

[…] test, the shrunken 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 […]


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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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