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GNomEx specifications

Information


Unique identifier OMICS_01005
Name GNomEx
Alternative name Genomic Experiment Data Repository and Core LIMS
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Genomic Experiment Data Repository and Core LIMS

GNomEx in publications

 (15)
PMCID: 5915807
PMID: 29707261
DOI: 10.1017/cts.2017.311

[…] internet browser., bam files were accessed using the bam.iobio [] sequence alignment inspector web app (http://bam.iobio.io) from the university of utah data laboratory information management system gnomex [], where links for all bam files are provided. quality metrics, including read coverage distribution, percentage of mapped reads, and duplication rate were inspected visually in the web […]

PMCID: 5829499
PMID: 29183906
DOI: 10.1242/bio.029512

[…] grant (c06 rr018928) to the j. david gladstone institutes and by the younger family fund (b.g.b.)., data availability , data are available at geo (gse59383) and at https://b2b.hci.utah.edu/gnomex/ (experiment 86r1)., supplemental data , supplementary information available online […]

PMCID: 5599515
PMID: 28912455
DOI: 10.1038/s41467-017-00667-5

[…] (sample “es” and “episc”), gse36114 (sample “endo_d6”, representing es cell for endoderm differentiation on day 6), gse69080 (“mes”, “hb”, “hp”), gse55310 (“he”), 7r2 (https://b2b.hci.utah.edu/gnomex/, sample “cp”, representing es cells differentiated to cardiac progenitors). the rna-seq data have been deposited in the ncbi gene expression omnibus (geo) database under accession code […]

PMCID: 5575285
PMID: 28851877
DOI: 10.1038/s41467-017-00405-x

[…] activity, except where rnapii chip-seq signal was lower than input., high throughput data are available on the cardiovascular development consortium server at https://b2b.hci.utah.edu/gnomex/. chip-seq and rna-seq data have also been deposited at geo under accession code gse93030., , jiahuan chen, yi fu and daniel s. day contributed equally to this work., electronic […]

PMCID: 5400508
PMID: 28394251
DOI: 10.7554/eLife.24570.023

[…] with: *p<0.05; **p<0.01; ***p<0.001., the high-throughput data used in this study are available through the cardiovascular development consortium server at https://b2b.hci.utah.edu/gnomex/. sign in as guest and go to experiment #410r. the data have also been deposited at geo (accession number gse73771)., this paper was supported by the following grants:, […]


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GNomEx institution(s)
Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA; Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA; Microarray/Next Generation Sequencing Shared Resource, Huntsman Cancer Institute, Salt Lake City, USA; Bioinformatics Shared Resource, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA

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