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Title: COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database

Abstract

We introduce COnTORT ( CO mprehensive T ranscriptomic OR ganizational T ool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream bioinformatic applications.

Authors:
ORCiD logo [1];  [1]; ORCiD logo [2]; ORCiD logo [3];
  1. Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
  2. Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA, Department of Civil &, Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
  3. Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA, Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1633687
Grant/Contract Number:  
SC0018409
Resource Type:
Published Article
Journal Name:
Microbiology Resource Announcements
Additional Journal Information:
Journal Name: Microbiology Resource Announcements Journal Volume: 9 Journal Issue: 25; Journal ID: ISSN 2576-098X
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English

Citation Formats

Myers, Kevin S., Place, Michael, Noguera, Daniel R., Donohue, Timothy J., and Putonti, ed., Catherine. COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. United States: N. p., 2020. Web. doi:10.1128/MRA.00587-20.
Myers, Kevin S., Place, Michael, Noguera, Daniel R., Donohue, Timothy J., & Putonti, ed., Catherine. COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. United States. https://doi.org/10.1128/MRA.00587-20
Myers, Kevin S., Place, Michael, Noguera, Daniel R., Donohue, Timothy J., and Putonti, ed., Catherine. Thu . "COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database". United States. https://doi.org/10.1128/MRA.00587-20.
@article{osti_1633687,
title = {COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database},
author = {Myers, Kevin S. and Place, Michael and Noguera, Daniel R. and Donohue, Timothy J. and Putonti, ed., Catherine},
abstractNote = {We introduce COnTORT ( CO mprehensive T ranscriptomic OR ganizational T ool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream bioinformatic applications.},
doi = {10.1128/MRA.00587-20},
journal = {Microbiology Resource Announcements},
number = 25,
volume = 9,
place = {United States},
year = {2020},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1128/MRA.00587-20

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Works referenced in this record:

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journal, January 2002


GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
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