The Sequence Reads and BAM Slicing tools, available in GDC 2.0, are powerful web-based resources for analyzing sequence reads.
Join us for a deep dive into GDC 2.0, where the focus is on empowering data scientists and developers to integrate their analysis tools with the Genomic Data Commons (GDC).
The GDC Gene Expression Clustering tool, available in GDC 2.0, is a web-based application for performing sample clustering by selecting a specific set of genes and visualizing the results as a heatmap of a z-score transformed matrix.
GDC 2.0 adopts a "cohort-centric" approach, allowing users to construct custom sets of cases and conduct gene- and variant-level data analysis directly within their web browser.
GDC 2.0 is a major update to the original GDC Data Portal introduced in 2016. This latest version adopts a “cohort-centric” workflow, in which users build custom sets of cases to analyze, and introduces several new gene- and variant-level analysis tools.
The Genomic Data Commons (GDC) provides the cancer research community with large quantities of molecular, clinical, and imaging data.
The Human Cancer Models Initiative (HCMI) is an international consortium with the goal of generating patient-derived next-generation cancer models (NGCMs) from diverse tumor types as a community resource.
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.
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.
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.
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.
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?
Researchers utilize an ever-increasing variety of molecular data types in their investigations of cancer and other complex diseases.
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.
Respect for, and protection of the interests of research participants are fundamental to NIH’s stewardship of human genomic and associated phenotypic data.
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.
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 of data from cancer genomic studies and makes harmonized data available to the research community through GDC data access tools.
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.
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.
The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that molecularly characterized over 11K cases spanning 33 cancer types.
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.
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.
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 DNA-Seq analysis pipeline identifies somatic variants within whole exome sequencing (WXS) and whole genome sequencing (WGS) data.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
The GDC provides Data Analysis, Visualization, and Exploration (DAVE) tools for exploring data from cancer genomic studies.
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.
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.
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.
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.