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TransVar specifications

Information


Unique identifier OMICS_21803
Name TransVar
Interface Web user interface
Restrictions to use None
Input data A file of identifiers, one identifier per line, case sensitive.
Input format TXT
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Ken Chen

Information


Unique identifier OMICS_21803
Name TransVar
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Ken Chen

Publication for TransVar

TransVar citations

 (3)
library_books

Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types

2016
BMC Genomics
PMCID: 4928158
PMID: 27356755
DOI: 10.1186/s12864-016-2727-x

[…] is critical to have consistent annotations from genomic to protein level. Zhou, et al. [] used COSMIC data to show that ambiguities frequently exist in variant annotation, and annotation tool such as TransVar [] would be very helpful to improve the accuracy of hotspot mutation prediction. In addition, further dissecting the mutation data into different cancer subtype groups (such as MSI and non-MS […]

library_books

Prevalence of alternative splicing choices in Arabidopsis thaliana

2010
BMC Plant Biol
PMCID: 3017808
PMID: 20525311
DOI: 10.1186/1471-2229-10-102

[…] verse sample types represented by publicly-available Arabidopsis ESTs from the dbEST database []. To aid in visualization and exploration of the results, we present a database and Web site http://www.transvar.org/arabitag that combines splicing choice frequency analysis with a visualization tool (Integrated Genome Browser []) that makes rapid and flexible visualization and inspection of alternativ […]

library_books

Consistency Analysis of Redundant Probe Sets on Affymetrix Three Prime Expression Arrays and Applications to Differential mRNA Processing

2009
PLoS One
PMCID: 2621337
PMID: 19165320
DOI: 10.1371/journal.pone.0004229

[…] at and viewed them in the Integrated Genome Browser, an open source, freely-available interactive desktop genome browser tool (http://igb.bioviz.org). The “link.psl” file is available from http://www.transvar.org/results/reanal/MOE430.trimmed.link.psl.In parallel, we obtained mRNA-to-genome alignments from the UCSC Genome Bioinformatics Web site using the Table Browser tool. mRNAs that mapped to a […]

Citations

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TransVar institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Khalifa Bin Zayed Al Nahyan Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Investigational Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
TransVar funding source(s)
Supported in part by the National Institutes of Health [grant numbers CA172652, CA168394, CA083639, CA143883, UL1 TR000371, P50 CA083639, U54 CA112970 and P50 CA098258], the MD Anderson Cancer Center Sheikh Khalifa Ben Zayed Al Nahyan Institute of Personalized Cancer Therapy, the Bosarge Family Foundation, the Mary K. Chapman Foundation, the Michael & Susan Dell Foundation (honoring Lorraine Dell) and the National Cancer Institute Cancer Center Support Grant [P30CA016672].

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