firehose_get protocols

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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

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  • person_outline Michael Noble <>

firehose_get in pipelines

 (3)
2018
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] snpdensity(r)=∑i#(snpiinri)∑ilength(ri), illumina infinium human dna methylation 450 level 3 data were downloaded from the broad tcga gdac (http://gdac.broadinstitute.org) using firehose_get. the coordinates of the methylation sites (hg18) were converted into hg38 using the ucsc liftover and further intersected with that of the core promoters (hg38). for each gene, […]

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

[…] 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 […]

2016
PMCID: 4917969
PMID: 27328849
DOI: 10.1038/ncomms12008

[…] picard and the genome analysis toolkit respectively. snps were called using the unified genotyper method of the genome analysis toolkit and annotated using annovar., tcga data were downloaded using firehose_get provided by the broad institute. scna data generated by the broad institute on the affymetrix genome-wide human snp array 6.0 from the 2015_02_04 run were used. we used copy-number […]


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firehose_get in publications

 (7)
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] 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 […]

PMCID: 5386646
PMID: 27821806
DOI: 10.18632/oncotarget.13095

[…] expression data of the “ovarian serous cystadenocarcinoma” data set were downloaded along with clinical data from the cancer genome atlas (tcga) data base (www.tcga-data.nci.nih.gov/tcga) using the “firehose-get“ command-line tool (https://confluence.broadinstitute.org/display/gdac/download). a detailed description of the clinical characteristics of the cohort can be found in a study by cancer […]

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

[…] 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” []. […]

PMCID: 5477496
PMID: 27116251
DOI: 10.1038/ncomms11452

[…] from broad firehose’s analyses runs. the putative copy-number calls were determined using gistic 2.0 (ref. ). the latest gistic analyses data were obtained using the following shell command: ‘firehose_get -o ‘gistic’ analyses latest laml’., the.cel files of affymetrix snp 6.0 data for gse21107 (ref. ) and gse23452 (ref. ) were downloaded from ncbi geo. the raw data were preprocessed using […]

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., detroit 562 cells were obtained from cell line service (cls), eppelheim, germany in may 2014 and hn […]


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