scholarly journals Author Correction: The NCI Genomic Data Commons

2021 ◽  
Author(s):  
Allison P. Heath ◽  
Vincent Ferretti ◽  
Stuti Agrawal ◽  
Maksim An ◽  
James C. Angelakos ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Commons

scholarly journals Uniform Genomic Data Analysis in the NCI Genomic Data Commons

2019 ◽  
Author(s):  
Zhenyu Zhang ◽  
Kyle Hernandez ◽  
Jeremiah Savage ◽  
Shenglai Li ◽  
Dan Miller ◽  
...  
Keyword(s):  
Methylation Status ◽  
Genomic Data ◽  
Data Repository ◽  
Sequencing Data ◽  
Data Types ◽  
Data Production ◽  
Number Variation ◽  
Data Portal ◽  
Data Commons ◽  
Human Genome Reference

AbstractThe goal of the National Cancer Institute (NCI) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive (https://gdc.cancer.gov/).

scholarly journals Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API

2017 ◽  
Vol 77 (21) ◽  
pp. e15-e18 ◽  
Author(s):  
Shane Wilson ◽  
Michael Fitzsimons ◽  
Martin Ferguson ◽  
Allison Heath ◽  
Mark Jensen ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Commons

The NCI Genomic Data Commons

2021 ◽  
Author(s):  
Allison P. Heath ◽  
Vincent Ferretti ◽  
Stuti Agrawal ◽  
Maksim An ◽  
James C. Angelakos ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Commons

scholarly journals GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

2017 ◽  
Author(s):  
Martin T. Morgan ◽  
Sean R. Davis
Keyword(s):  
High Performance ◽  
Data Transfer ◽  
Cancer Genomics ◽  
Genomic Data ◽  
Software Project ◽  
Link Type ◽  
Open Development ◽  
Statistical Programming ◽  
Basic Infrastructure ◽  
Data Commons

AbstractThe National Cancer Institute (NCI) Genomic Data Commons (Grossman et al. 2016, https://gdc.cancer.gov/) provides the cancer research community with an open and unified repository for sharing and accessing data across numerous cancer studies and projects via a high-performance data transfer and query infrastructure. The Bioconductor project (Huber et al. 2015) is an open source and open development software project built on the R statistical programming environment (R Core Team 2016). A major goal of the Bioconductor project is to facilitate the use, analysis, and comprehension of genomic data. The GenomicDataCommons Bioconductor package provides basic infrastructure for querying, accessing, and mining genomic datasets available from the GDC. We expect that Bioconductor developer and bioinformatics community will build on the GenomicDataCommons package to add higher-level functionality and expose cancer genomics data to many state-of-the-art bioinformatics methods available in Bioconductor.Availabilityhttps://bioconductor.org/packages/GenomicDataCommons & https://github.com/seandavi/GenomicDataCommons.

scholarly journals Genomic Data Commons ushers in new era for information sharing

Cancer ◽  
2016 ◽  
Vol 122 (18) ◽  
pp. 2777-2778 ◽  
Author(s):  
Carrie Printz
Keyword(s):  
Information Sharing ◽  
Genomic Data ◽  
New Era ◽  
Data Commons

scholarly journals Uniform genomic data analysis in the NCI Genomic Data Commons

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhenyu Zhang ◽  
Kyle Hernandez ◽  
Jeremiah Savage ◽  
Shenglai Li ◽  
Dan Miller ◽  
...  
Keyword(s):  
Methylation Status ◽  
Genomic Data ◽  
Data Repository ◽  
Sequencing Data ◽  
Data Types ◽  
Data Production ◽  
Number Variation ◽  
Data Portal ◽  
Data Commons ◽  
Human Genome Reference

AbstractThe goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive (https://gdc.cancer.gov/).

scholarly journals GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC

2017 ◽  
Author(s):  
Ruidong Li ◽  
Han Qu ◽  
Shibo Wang ◽  
Julong Wei ◽  
Le Zhang ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Large Scale ◽  
Genomic Data ◽  
Regulatory Mechanisms ◽  
Omics Data ◽  
Bioconductor Package ◽  
Competing Endogenous Rnas ◽  
Downstream Analysis ◽  
User Friendly ◽  
Data Commons

AbstractThe large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, to facilitate downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.AvailabilityGDCRNATools is an R/Bioconductor package that is freely available at https://github.com/Jialab-UCR/GDCRNATools

scholarly journals Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

Cell Systems ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 24-34.e10 ◽  
Author(s):  
Galen F. Gao ◽  
Joel S. Parker ◽  
Sheila M. Reynolds ◽  
Tiago C. Silva ◽  
Liang-Bo Wang ◽  
...  
Keyword(s):  
Genomic Data ◽  
Before And After ◽  
Data Commons
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