chimerascan pipeline

chimerascan specifications

Information


Unique identifier OMICS_01343
Name chimerascan
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTQ
Output format TSV/HTML
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.5
Stability Stable
Requirements bowtie
Maintained Yes

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Documentation


Maintainer


  • person_outline Christopher A. Maher <>

Additional information


https://code.google.com/archive/p/chimerascan/wikis/HowChimerascanWorks.wiki

Publication for chimerascan

chimerascan IN pipeline

2016
PMCID: 5137021
PMID: 27917920
DOI: 10.1038/srep38397

[…] to the formula:, , p-values were calculated using the perl module comparison based on poisson distribution82, and probability values were obtained using the r package noiseq83., tophat281 and chimerascan84 (v0.4.5) were used to identify alternative splicing and gene fusion events, according to the protocols, respectively., gene ontology terms for mrnas enriched in evs and kegg pathway […]

chimerascan institution(s)
Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
chimerascan funding source(s)
Supported by Department of Defense Breast Cancer Predoctoral Grant; Prostate Cancer Foundation Young Investigator Award and National Institutes of Health Pathway to Independence (K99 CA149182-01) Award; National Institutes of Health, Department of Defense and Early Detection Research Network.

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