GENE-E pipeline

GENE-E specifications

Information


Unique identifier OMICS_15859
Name GENE-E
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Mac OS, Windows
Programming languages Java, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Joshua Gould <>

GENE-E IN pipelines

 (15)
2018
PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] at a 10% false-discovery rate (fdr) with a q value of <0.05. among these genes, only those with average rpkm ratios of ≥1.5 were counted as changed in expression., heat maps were generated using gene e (https://software.broadinstitute.org/gene-e/index.html). venn diagrams were created using biovenn (41)., gsea software, available through the broad institute […]

2017
PMCID: 5305113
PMID: 28192534
DOI: 10.1371/journal.pone.0171677

[…] z-score statistic was used to predict the directional effect of one molecule on another or on a process to predict the activation state (inhibition/activation). heat maps were generated using gene-e (broad institute, https://software.broadinstitute.org/gene-e/)., sequencing run data containing base call information was stored and demultiplexed in basespace® sequence hub. the resulting […]

2017
PMCID: 5305113
PMID: 28192534
DOI: 10.1371/journal.pone.0171677

[…] effect of one molecule on another or on a process to predict the activation state (inhibition/activation). heat maps were generated using gene-e (broad institute, https://software.broadinstitute.org/gene-e/)., sequencing run data containing base call information was stored and demultiplexed in basespace® sequence hub. the resulting fast.gz files were decompressed using 7-zip to obtain fastq […]

2017
PMCID: 5392273
PMID: 28407681
DOI: 10.18632/oncotarget.15381

[…] the geo under accession codes gse85857. in addition, mrna expression data was uploaded to ipa (www.ingenuity.com) and analyzed using default parameters. the expression heat map was generated using gene-e (broad institute, ma, usa www.broadinstitute.org/cancer/software/gene-e/). fifty-eight emt genes were selected by using the list from [50, 51]., runx1 chip-qpcr was performed essentially […]

2017
PMCID: 5392273
PMID: 28407681
DOI: 10.18632/oncotarget.15381

[…] was uploaded to ipa (www.ingenuity.com) and analyzed using default parameters. the expression heat map was generated using gene-e (broad institute, ma, usa www.broadinstitute.org/cancer/software/gene-e/). fifty-eight emt genes were selected by using the list from [50, 51]., runx1 chip-qpcr was performed essentially as described [52]. briefly, 200,000 mcf10a cells were cross-linked, lysed […]

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