AVISPA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool AVISPA
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Tool usage distribution map

This map represents all the scientific publications referring to AVISPA per scientific context
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Associated diseases

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Popular tool citations

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AVISPA specifications

Information


Unique identifier OMICS_16615
Name AVISPA
Alternative name Advanced Visualization of Splicing Prediction and Analysis
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Yoseph Barash

Publication for Advanced Visualization of Splicing Prediction and Analysis

AVISPA citations

 (3)
library_books

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation

2017
PLoS Biol
PMCID: 5636171
PMID: 28961236
DOI: 10.1371/journal.pbio.2002623

[…] ters were used, with a filter option applied to require a minimum of 20 reads to support an event identification.To identify regulatory elements that may affect retention of EIF2B5 intron 12, we used AVISPA []. This method, based on computationally derived splicing codes, has been used previously to detect and experimentally verify novel regulators of exon splicing in a variety of experimental con […]

library_books

Integrative deep models for alternative splicing

2017
Bioinformatics
PMCID: 5870723
PMID: 28882000
DOI: 10.1093/bioinformatics/btx268

[…] odels, we use it to compare the old and new models. We generated genomic features and PSI quantification for ∼12 000 cassette exons used in () for this dataset for the five tissues using MAJIQ () and AVISPA (). The second dataset, denoted MGP Data, was prepared by () and it contains RNA-Seq data from six tissues (heart, hippocampus, liver, lung, spleen and thymus) with average read coverage of 60 […]

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A new view of transcriptome complexity and regulation through the lens of local splicing variations

2016
eLife
PMCID: 4801060
PMID: 26829591
DOI: 10.7554/eLife.11752.080

[…] inclusion from P15 through adulthood (). Taken together, this complex LSV offers a novel mechanism for postnatal neuronal reduction in Ptbp1.To identify putative regulators of novel exon 14, we used AVISPA (), a web tool that utilizes splicing code models to suggest motifs important for tissue-specific splicing, and identified the [U]GCAUG binding motif of the Rbfox family as important for neuron […]


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AVISPA institution(s)
Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA; Universitat Pompeu Fabra, Barcelona, Spain; Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
AVISPA funding source(s)
Supported by FPI grant from the Spanish Ministry of Science; NSERC Steacie and CIHR grants, the University of Toronto, an OGI Spark grant and a Genome Canada grant.

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