TCGA_dbGaP statistics

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TCGA_dbGaP specifications

Information


Unique identifier OMICS_18627
Name TCGA_dbGaP
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Some TCGA project ID, file ID, case ID, disease type or experiment strategy.
Input format PY, CSV
Output data Reads from genomic region of interest.
Output format SAM, CSV
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
https://github.com/NCBI-Hackathons/TCGA_dbGaP/archive/master.zip
Maintained Yes

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TCGA_dbGaP in publications

 (5)
PMCID: 5538035
PMID: 28794857
DOI: 10.5256/f1000research.10605.r21260

[…] and a user-friendly gui. feature requests or contributions of code can be made on our github site, which will be monitored for such activity., latest source code: https://github.com/ncbi-hackathons/tcga_dbgap., archive source code as at the time of publication: doi, 10.5281/zenodo.160551 (kurata, 2016) ( https://zenodo.org/record/160551#.we7lz9wltcs), license: cc0 1.0 universal, we would like […]

PMCID: 5013272
PMID: 27600471
DOI: 10.1038/srep32512

[…] were measured with agilent 44 k. (3) nb93 consists of 93 caucasian adjacent normal breast samples from tcga. birdseed processed germline genotype data from the affy6 snp array were obtained from the tcga dbgap data portal. (4) bc765 consists of 765 caucasian breast tumour samples from tcga. gene expression levels were assayed by rna sequencing, rsem (rnaseq by expectation-maximization) […]

PMCID: 4906168
PMID: 27279334
DOI: 10.1038/ncomms11548

[…] the censor time was randomly sampled from 10 to 90% of the actual death time., we obtained the rna-seq read counts and clinical parameters of 682 idc patients from tcga breast cancer (brca) cohort (tcga dbgap accession id phs000178). the rna-seq reads were mapped to the human genome and transcriptome by the tcga consortium using burrows-wheeler aligner (bwa) with default settings. the tcga […]

PMCID: 4853421
PMID: 27117709
DOI: 10.1038/ncomms11375

[…] 55 undefined breast tumours; all non-european samples (as determined by clustering and pca) were excluded from this analysis. germline genotype data from affymetrix snp 6 array were obtained from tcga dbgap data portal. gene expression levels for the breast tumours were assayed by rna sequencing, rsem (rnaseq by expectation-maximization21) normalized per gene, as obtained from the tcga […]

PMCID: 4628784
PMID: 26521025
DOI: 10.1186/s13073-015-0230-7

[…] in dogs suggests a potential route for developing anti-lymphoma strategies based on dog therapeutic trials., computational analysis was performed on multiple sets of rnaseq data, including 116 tcga dbgap dlbcl tumor samples (dbgap accession number phs000235.v6.p1 – dbgap approval for this specific project was granted). the eight normal b-cell (four naïve b cells and four germinal center b […]


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