eagle-i University of PennsylvaniaUniversity of Pennsylvania
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BioCiphers Lab

Summary:

The lab combines genomic and genetic data to computationally model RNA processing, followed by experimental verification to decipher post-transcriptional regulation, phenotypic diversity and disease

Affiliations:

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Software

  • AVISPA ( Algorithmic software suite )

    AVISPA is a web tool that enables both prediction and splicing analysis of alternative and tissue-dependent exons in any gene of interest. Given an exon, the tool predicts whether it is alternative and whether its inclusion is expected to change in different tissues. It reports whether the exon is known to be alternative based on an internal transcripts database, and performs in silico splicing analysis, identifying putative regulatory elements and mapping those as tracks in the genome browser.

    AVISPA currently supports analysis on the mouse mm10 genome build.

  • MAJIQ ( Algorithmic software suite )

    "MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data. Conceptually, MAJIQ/Voila can be divided into three modules:

    MAJIQ Builder: Uses RNA-Seq (BAM files) and a transcriptome annotation file (GFF3) to define splice graphs and known/novel Local Splice Variations (LSV).

    MAJIQ Quantifier: Quantifies relative abundance (PSI) of LSVs and changes in relative LSV abundance (delta PSI) between conditions w/wo replicates.

    Voila: A visualization package that combines the output of MAJIQ Builder and MAJIQ Quantifier using interactive D3 components and HTML5. Voila creates interactive summary files with gene splice graphs, LSVs, and their quantification."


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Last updated: 2015-11-03T11:22:17.628-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016