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firehose_get specifications

Information


Unique identifier OMICS_19000
Name firehose_get
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 0.4.8
Stability Stable
Maintained Yes

Download


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Versioning


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Maintainer


  • person_outline Michael Noble

firehose_get citations

 (4)
library_books

Probing instructions for expression regulation in gene nucleotide compositions

2018
PLoS Comput Biol
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] /www.univ-montp3.fr/miap/~lebre/IBCRegulatoryGenomics.Isoform expression data (.rsem.isoforms.normalized_results files) were downloaded from the Broad TCGA GDAC (http://gdac.broadinstitute.org) using firehose_get. We collected data for 73599 isoforms in 225 samples of the 241 initially considered. All the genes and isoforms not detected (no read) in any of the considered samples were removed from […]

library_books

Crosstalk between the mitochondrial fission protein, Drp1, and the cell cycle is identified across various cancer types and can impact survival of epithelial ovarian cancer patients

2016
Oncotarget
PMCID: 5312366
PMID: 27509055
DOI: 10.18632/oncotarget.11047

[…] ata was downloaded from the European Genome-phenome Archive (EGA; https://www.ebi.ac.uk/ega/home; accession EGAD00001000877). GISTIC data was downloaded from Broad Institute's firehose pipeline using firehose_get script (https://confluence.broadinstitute.org/display/GDAC/Download).TCGA EOC patients were clinically classified based on their reported “ProgressFreeStatus” and “PlatinumStatus” []. 33 […]

library_books

MERTK as a novel therapeutic target in head and neck cancer

2016
Oncotarget
PMCID: 5078043
PMID: 27081701
DOI: 10.18632/oncotarget.8724

[…] [] were downloaded from the TCGA Genome Data Analysis Center (GDAC) Firehose website (https://confluence.broadinstitute.org/display/GDAC/Home)(http://ezid.cdlib.org/id/doi:10.7908/C19P30S6) using the firehose get data-retrieval utility from the 04 February 2015 standard data and analyses run. […]

library_books

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types

2015
PLoS One
PMCID: 4640835
PMID: 26555223
DOI: 10.1371/journal.pone.0142618

[…] All data were downloaded using the Broad Institute’s firehose_get data-retrieval utility. To maintain the coherency of the analysis across different data layers and cancer types, we used Level 3 normalized molecular data as the input to our analysis and […]

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