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MAJIQ

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/00000152-a7d5-3005-b71f-cc9580000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Resource Description
    "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: <strong>MAJIQ Builder</strong>: Uses RNA-Seq (BAM files) and a transcriptome annotation file (GFF3) to define splice graphs and known/novel Local Splice Variations (LSV). <strong>MAJIQ Quantifier</strong>: Quantifies relative abundance (PSI) of LSVs and changes in relative LSV abundance (delta PSI) between conditions w/wo replicates. <strong>Voila</strong>: 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."
  2. Used by
    BioCiphers Lab
  3. Operating System
    LINUX
  4. Data Input
    BAM files from RNA-seq experiments
  5. Data Input
    GFF3 annotation file
  6. Data Output
    Splice graphs for each gene
  7. Data Output
    All detected single source and single targets local splicing variations per gene
  8. Data Output
    Quantification of local splicing variations
  9. Data Output
    Changes in local splicing variations quantification between two conditions
  10. Software purpose
    Transcript splicing prediction objective
  11. Related Publication or Documentation
    A new view of transcriptome complexity and regulation through the lens of local splicing variations
  12. Website(s)
    http://majiq.biociphers.org/
  13. Related Technique
    Bioinformatics analysis
  14. Related Technique
    RNA sequencing
  15. Coded in
    Python
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2016-02-03T11:16:13.457-05:00
  4. creator
    fcoldren
  5. modified
    2016-02-03T11:55:44.671-05:00

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