GDC Webinars

Past Webinars

Downloading Large Data Sets from the GDC

Date: Monday, October 23, 2023

Time: 2:00 PM - 2:30 PM (EDT)

Location: Web Conference (See WebEx information below)

The Genomic Data Commons (GDC) provides the cancer research community with large quantities of molecular, clinical, and imaging data. To support the high volumes of data transfer and the varying needs and resources of users, the GDC provides a variety of methods for data transfer, such as the GDC Data ...

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GDC BAM Slicing

Date: Monday, June 26, 2023

Time: 2:00 PM - 2:30 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC provides a “BAM slicing” feature that lets users download specific parts of a Binary Alignment Map (BAM) file instead of the whole file. Users specify the subset of a BAM file for downloading by providing genome coordinates, gene symbols, or requesting unmapped reads. BAM slicing is an efficient ...

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Overview of the GDC API

Date: Monday, March 27, 2023

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC Application Programming Interface (API) drives GDC data access, analysis, and submission tools and provides programmatic access to GDC functionality. This webinar will provide an overview of the GDC API and associated endpoints for searching, downloading, and analyzing data. An interactive demonstration of the GDC API using Jupyter Notebooks ...

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GDC Data Model and Data Dictionary Overview and Updates

Date: Monday, January 30, 2023

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

Understanding the structure and content of data at the GDC can help users access, submit, or analyze data at the GDC. The GDC uses a graph-based data model that maintains a relationship between a case, biospecimen, clinical, and submitted data files. Properties within the model are defined in the ...

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Example Use Cases for Harmonized Data in the GDC

Date: Monday, November 14, 2022

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC harmonizes raw sequencing data from cancer genomic studies by aligning to a common reference genome (GRCh38) and applying bioinformatics methods for generating high-level data such as mutation calls and structural variants. Example use cases for this data include helping to identify high and low frequency cancer drivers, ...

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GDC Frequently Asked Questions (FAQs)

Date: Monday, August 29, 2022

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Do you know how the GDC calculates survival for Kaplan-Meier curves? Or how to find data associated with a visualization in the GDC Data Portal? And how do you obtain access to controlled data that the GDC supports? This webinar will review FAQs at the GDC involving data access, ...

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Processing Whole Genome, Methylation, and Copy Number Data Types at the GDC

Date: Monday, June 6, 2022

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Researchers utilize an ever-increasing variety of molecular data types in their investigations of cancer and other complex diseases. To support the research community, the GDC processes and hosts a variety of data types, including whole genome sequencing, methylation, protein expression, copy number, and other miscellaneous data types. At this ...

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GDC GENCODE v36 Update

Date: Monday, April 11, 2022

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

One of the main goals of the Genomic Data Commons is to provide useful and up-to-date genomic data for the cancer research community. Since its launch in 2016, the GDC has used GENCODE v22 as the reference gene model for bioinformatic analyses. To keep up with continually evolving ...

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Obtaining Access to Controlled Data in the GDC

Date: Monday, January 31, 2022

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

Respect for, and protection of the interests of research participants are fundamental to NIH’s stewardship of human genomic and associated phenotypic data. Access to controlled data in the GDC requires an NIH eRA Commons account and authorization through NIH’s Database of Genotypes and Phenotypes (dbGaP). This webinar will ...

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GDC Data Download and Upload Strategies

Date: Monday, November 29, 2021

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The Genomic Data Commons (GDC) provides the cancer research community with large quantities of molecular, clinical, and imaging data in around 18 different formats. The GDC also accepts data from the community to be processed via GDC bioinformatics pipelines and shared. To support the high volumes of data transfer and ...

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GDC Single Cell RNA-Seq Support

Date: Monday, September 27, 2021

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Single-cell RNA-Seq (scRNA-Seq) is a valuable tool for studying tumor heterogeneity and also the microenvironment, which may be composed of a distinct cancer subclones along with immune and other cell types. The GDC supports the submission and harmonization of tumor scRNA-Seq data and makes the data ...

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GDC Data Submission Overview

Date: Monday, June 28, 2021

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC supports the submission of data from cancer genomic studies and makes harmonized data available to the research community through GDC data access tools. This webinar will provide an overview of GDC data submission, guide the submitter through step-by-step procedures for data upload, and demonstrate data submission ...

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Using the GDC API

Date: Monday, April 26, 2021

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC Application Programming Interface (API) drives GDC data access, analysis, and submission tools and provides programmatic access to GDC functionality. This webinar will provide an overview of the GDC API and associated endpoints for searching, downloading, analyzing, and submitting data. An interactive demonstration of the GDC API using Jupyter ...

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GDC Overview

Date: Monday, March 29, 2021

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The NCI Genomic Data Commons (GDC) is a knowledge system for cancer that helps researchers share and access genomic, clinical, and biospecimen data and facilitates precision oncology. This webinar will provide an overview of the GDC, introduce some of GDC’s tools for accessing, analyzing, visualizing, and submitting data, and ...

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TCGA Resources Available in the GDC

Date: Monday, February 22, 2021

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that molecularly characterized over 11K cases spanning 33 cancer types. Available data includes: clinical, biospecimen, slide images, WGS/WXS/RNA/miRNA alignments, WXS somatic mutations, gene/isoform/miRNA expression quantification, copy number data, and methylation values. This webinar will ...

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GDC Open Office

Date: Monday, January 25, 2021

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC provides the cancer research community with a unified repository and cancer knowledge base that enables data sharing across cancer genomic studies in support of precision medicine. The GDC enables access to data from 67 projects, 23 K+ genes, and 3.28 M+ mutations. Data is processed using GDC ...

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GDC Data Quality

Date: Monday, November 30, 2020

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC provides the cancer research community with a unified repository and cancer knowledge base that enables data sharing across cancer genomic studies in support of precision medicine. As a data sharing knowledge base, ensuring access to high quality data is imperative. This requires a strategy that employs data quality ...

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GDC About the Data

Date: Monday, October 19, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC is a unified repository and cancer knowledge base that enables data sharing across cancer genomic studies in support of precision medicine. The GDC provides access to clinical and genomic data from 65+ projects through supported cancer research programs and organizations that contribute data to the GDC. This webinar ...

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GDC DNA-Seq Data Processing

Date: Monday, September 28, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC DNA-Seq analysis pipeline identifies somatic variants within whole exome sequencing (WXS) and whole genome sequencing (WGS) data. Somatic variants are identified by comparing allele frequencies in normal and tumor sample alignments, annotating each mutation, and aggregating mutations from multiple cases. This webinar will provide an in depth ...

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GDC RNA-Seq Data Processing

Date: Monday, July 27, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

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 performed on the aligned reads. This webinar will provide an in depth ...

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GDC Documentation and Publications

Date: Monday, June 29, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC Web Site and Documentation Site provide useful information on GDC data access, submission, analysis, and processing. The GDC also makes publications and associated data available on the GDC Web Site. This webinar will demonstrate GDC documentation and publication resources, and show how users can access valuable information on ...

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GDC Use Case: Analyzing a Cohort

Date: Thursday, May 28, 2020

Time: 12:00 PM - 1:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC allows users to build a cohort, perform detailed analysis on the cohort, and download the associated data. This webinar will demonstrate a complete use case demonstrating GDC data analysis, visualization, and exploration features in support of cancer research....

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GDC Data Transfer Tool (DTT)

Date: Monday, April 27, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Raw sequence data, stored as BAM files, make up the bulk of data stored at the GDC. Most BAM files stored in the GDC are in the 50 MB - 40 GB size range, with some of the whole genome BAM files reaching sizes of 200-300 GB. The GDC Data ...

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GDC Biospecimen, Clinical, and Experiment Data Model

Date: Monday, March 30, 2020

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC employs a graph based data model that maintains the relationship between a case, biospecimen, clinical, and submitted data files. Properties within the graph model are defined in the GDC Data Dictionary. This webinar will review the GDC Data Model and GDC Data Dictionary and demonstrate how to perform ...

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GDC Clinical Data Analysis

Date: Monday, February 24, 2020

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC Clinical Data Analysis feature allows users to examine the clinical data for a case set in more detail. Users can select which clinical variables they want to display and visualize the data using various supported plot types. This webinar will demonstrate how to select clinical variables for a ...

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GDC Data Submission Demonstration

Date: Monday, January 27, 2020

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC supports the submission of data from cancer genomic studies and makes submitted data available to the research community through GDC data access tools. This webinar will guide submitters through the GDC submission process by demonstrating file upload, submission review/QC, and request for harmonization through GDC Submission Tools....

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GDC API and Apps

Date: Monday, December 16, 2019

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC Application Programming Interface (API) drives GDC data access and submission tools and provides programmatic access to GDC functionality. This includes searching for, downloading, and submitting data and metadata. This webinar will provide an overview of the API endpoints, and demonstrate how GDC applications use the API....

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GDC Data Submission

Date: Monday, November 25, 2019

Time: 2:00 PM - 3:00 PM (EST)

Location: Web Conference (See WebEx information below)

The GDC supports the submission of data from cancer genomic studies and makes submitted data available to the research community through GDC data access tools. This webinar will provide an overview of the GDC and the types of data accepted, walk through the GDC submission process and associated tools, introduce ...

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GDC Bioinformatics Pipelines

Date: Monday, September 30, 2019

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC bioinformatics pipelines support the alignment of DNA and RNA sequence data against a common reference genome build, and the generation of derived data. GDC pipelines are implemented using data processing software and algorithms selected in consultation with the expert genomics community. This webinar will provide an overview of ...

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GDC Data Analysis, Visualization, and Exploration (DAVE) Tools

Date: Monday, August 26, 2019

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The GDC provides Data Analysis, Visualization, and Exploration (DAVE) tools for exploring data from cancer genomic studies. This webinar will provide an overview of GDC DAVE tools for exploring most frequently mutated genes and mutations, performing a survival analysis for cases with and without these mutations, viewing the distribution of ...

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GDC Overview

Date: Thursday, July 25, 2019

Time: 12:00 PM - 1:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The NCI Genomic Data Commons (GDC) is a knowledge base for cancer that promotes sharing of genomic, clinical, and biospecimen data between researchers and facilitates precision medicine in oncology. This webinar will provide an overview of the GDC and GDC applications and interfaces supporting data access, submission, and analysis....

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Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools

Date: Thursday, October 12, 2017

Time: 12:00 PM - 1:00 PM (EDT)

Location: Web Conference (See WebEx information below)

The Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools webinar will help introduce users to GDC tools for analyzing data from cancer genomic studies. As an example, we will explore most frequently mutated genes and mutations and perform a survival analysis for cases with and without these ...

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Querying and Downloading Data using the GDC Data Portal and the GDC Data Transfer Tool

Date: Thursday, February 2, 2017

Time: 12:00 PM - 1:00 PM (EST)

Location: Web Conference (See WebEx information below)

The Querying and Downloading Data using the GDC Data Portal and the GDC Data Transfer Tool webinar will help introduce users to the GDC tools for downloading and retrieving data from cancer genomic studies. As an example, we will query and download open access data using the GDC Data Portal ...

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Navigating the GDC - A Case Study

Date: Thursday, November 17, 2016

Time: 12:00 PM - 1:00 PM (EST)

Location: Web Conference

The Navigating the GDC - A Case Study webinar is the first webinar in a series of NCI GDC Webinars. This webinar will help introduce users to the different GDC tools and data types that are available to support cancer genomic analysis. As an example, we will identify common p53 mutations ...

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