Bethesda, MD
Repositories
Trans NIH Facility
The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...
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Bioinformatics
10/19/2020 - Register This webinar is intended for cancer researchers who are interested in learning more about the data that is available in the NCI Genomic Data Commons (GDC).The GDC is a unified repository that Read More...
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Bioinformatics
The Genomic Data Commons is well documentated. If you need help, checking the documentation is a good first step. If you need additional help with accessing, downloading, submitting, or analyzing data in the GDC, contact Read More...
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Bioinformatics
06/06/2022 - Are you a cancer researcher or bioinformatician wanting to learn more about how the experts at NCI’s Genomic Data Commons (GDC) process a variety of molecular data types? This month’s GDC support Read More...
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Bioinformatics
The Genomic Data Commons (GDC) is a repository and computational resource for cancer genomic data and associated clinical and related information. The GDC includes data from 22 programs (including TCGA), 83 projects, 69 primary sites, and 44,637 cases. Genomic Read More...
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Bioinformatics
10/23/2023 - Do you use the Cancer Research Data Commons’ (CRDC’s) Genomic Data Commons (GDC) for downloading molecular, clinical, and/or imaging data? Do you download large quantities of data? Attend Read More...
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Bioinformatics
11/14/2022 - During this webinar, the Genomic Data Commons ’ (GDC’s) Drs. Zhenyu Zhang and Bill Wysocki will review the different types of harmonized data that the GDC makes available for the cancer research community. The Read More...
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Bioinformatics
The TCGA data within the GDC are harmonized. Use these resources to understand more about the data, including the many codes used. Note Legacy datasets, datasets not aligned to GRCh38, and data from the original Read More...
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Bioinformatics
04/22/2024 - Intended Audience This webinar targets researchers interested in exploring genomic mutation analysis capabilities within the recently introduced NCI Genomic Data Commons (GDC) 2.0 platform. It aims to accommodate individuals interested in analyzing genes and mutations Read More...
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Bioinformatics
01/30/2023 - Are you interested in accessing cancer data from genomics studies? If so, register for this NCI webinar to learn more about the Genomic Data Commons (GDC)! University of Chicago’s Dr. Bill Wysocki will Read More...
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Bioinformatics
Navigate to Helix, the interactive data transfer and file management node for the NIH HPC Systems. ssh username@helix.nih.gov Navigate to your data directory and create a new directory for the data to Read More...
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Bioinformatics
Navigate to the GDC Data Portal at https://portal.gdc.cancer.gov/ To select your cases of interest, you can navigate to "Projects" or "Cohort Builder" Let's use breast cancer Read More...
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Bioinformatics
Note This tutorial uses the command line client; to use the Data Transfer GUI, see here. The GDC Application Programming Interface (API) can also be used to search for, download, and submit data and metadata. Read More...
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Bioinformatics
BAM Slicing Download Slice individual BAM files based on the variant, gene, position, or SNPs for individual cases/entities Download unmapped reads from a BAM file Clinical Data Analysis Visualize clinical data with histograms, survival Read More...
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Bioinformatics
11/29/2021 - Speaker: Bill Wysocki, Ph.D , Director of User Services and Outreach for the GDC at the University of Chicago. The NCI Genomic Data Commons’s (GDC) November webinar will show researchers how to both Read More...
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Bioinformatics
03/29/2021 - Register/Join The NCI Genomic Data Commons' (GDC's) upcoming webinar will introduce new users to its portal and library of computational resources. GDC experts will also answer questions about the GDC and genomic Read More...
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Bioinformatics
11/30/2020 - Register As the genomic data-specific repository within NCI's Cancer Research Data Commons (CRDC), the GDC provides cloud-based access to some of the largest and most comprehensive cancer genomic data sets as well as Read More...
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Bioinformatics
The GDC allows you to perform some analyses on cancer data spanning multiple programs and projects. You can perform similar tasks and other advanced tasks using other data platforms. However, you may want to download Read More...
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Bioinformatics
06/26/2023 - In this webinar, University of Chicago’s Dr. Bill Wysocki will demonstrate the NCI Genomic Data Commons’ (GDC’s) Binary Alignment Map (BAM) slicing feature. If you use Read More...
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Bioinformatics
09/27/2021 - The NCI Genomic Data Commons’ (GDC) September webinar will introduce cancer researchers and bioinformaticians to the GDC's single-cell RNA-Seq (scRNA-Seq) data workflow. Single cell sequencing is a powerful platform for studying tumor heterogeneity Read More...
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Bioinformatics
09/28/2020 - Register/Join This webinar is intended for cancer researchers and bioinformaticians who are interested in learning more about the NCI Genomic Data Commons’ (GDC’s) bioinformatics pipelines for data harmonization. The GDC DNA-Seq analysis Read More...
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Bioinformatics
01/27/2020 - Learn about the GDC's submission process and tools. Get a demonstration of how to upload and review data.
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Bioinformatics
Like many large projects, there are variations of data available. Let's clear up some confusion and define the following: Harmonized data Data aligned to GRCh38 and data further proccessed using standard pipelines featuring open-source Read More...
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Bioinformatics
06/18/2024 - The Cancer Genome Atlas (TCGA) was a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. This resulted in a massive open-source dataset that continues to Read More...
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Bioinformatics
07/27/2020 - The GDC RNA-Seq Analysis pipeline quantifies protein-coding gene expression. RNA-Seq data is aligned to the reference genome to detect splice junctions and then re-aligned to increase quality. Gene expression quantification and fusion detection are Read More...
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Bioinformatics
Learners will Discover public resources for accessing, analyzing, and downloading TCGA data. Learn about features of the NCI Genomic Data Commons Data Portal. Understand how to download TCGA data from the GDC.
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CREx News & Updates April 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...
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Bioinformatics
03/13/2024 - Dear Colleagues, UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from Read More...
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Bioinformatics
10/31/2022 - UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as well as Read More...
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Bioinformatics
Note This is not an exhaustive list. cBioPortal cBioPortal is a platform for exploratory and interactive visualization, analysis, and download of cancer genomics data. With cBioPortal You can quickly view genomic alterations across a set Read More...
Rockville, MD
Repositories
Trans NIH Facility
Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, Read More...
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Bioinformatics
05/26/2021 - Register Description: This webinar will highlight UCSC Xena's newest features including genome-wide differential gene expression analysis, violin plots, and a simpler way to filter and subgroup. UCSC Xena ( http://xena.ucsc.edu/ ) is Read More...
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Bioinformatics
05/19/2020 - UCSC Xena ( xena.ucscedu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as Read More...