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New Single Cell RNA-Seq Tool and CNV Categories Available in the GDC Data Portal

The GDC 2.4 Röntgen Release brings a range of new features aimed at enhancing data analysis and user experience.

  • Single Cell RNA-Seq Tool: Researchers can now analyze single-cell RNA-Seq data through cluster plots and gene expression overlays. Key features include visualization of dimensionality reduction plots such as UMAP, t-SNE, and PCA, differential gene expression analysis, gene set enrichment analysis, and a violin plot summarizing the data. For a complete list of features, refer to the Portal documentation. Instructions for utilizing the scRNA-Seq API are available in the API documentation. 
  • Expanded CNV Categories: The GDC now offers enhanced CNV categories, with more specific values. Gains are now classified by "gain" or "amplification" while losses are categorized as "heterozygous loss" and "homozygous loss". Additional details can be found in the API and Portal documentation.
  • BAM Metrics in File Summaries: Quality control metrics from aligned reads are now displayed in File Summaries for genomic BAMs, providing key insights into sequencing quality.
  • Enhanced Sample Sheet: The updated sample sheet includes new sample properties such as tissue type, tumor descriptor, specimen type, and preservation method. Download options are now more accessible.
  • Additional Clinical Attributes: Clinical JSON/TSV downloads now feature expanded case and other clinical attributes for comprehensive data analysis.
  • Improved Cohort Builder: The Cohort Builder search functionality has been refined to better guide users to relevant results.

This release honors the legacy of Wilhelm Röntgen, continuing the GDC tradition of celebrating pioneering scientists.

For detailed information, visit the GDC Data Portal Release Notes. Updated documentation and tutorials are available in the GDC 2.0 Data Portal User’s Guide and accompanying GDC 2.0 Video Tutorial.

We value your feedback! Share your thoughts on GDC 2.0 by contacting us at support@nci-gdc.datacommons.io.

Wilhelm Röntgen
Wilhelm Röntgen National Library of Medicine

In 1895, German physicist Wilhelm Röntgen discovered "a new kind of ray capable of traveling long distances, penetrating solid objects, activating fluorescent screens, and exposing photographic plates" while experimenting with a cathode ray tube in his laboratory. For this groundbreaking discovery of the X-ray, he was awarded the first Nobel Prize in Physics in 1901.

Photo and content courtesy of the National Library of Medicine: https://www.nlm.nih.gov/exhibition/visibleproofs/galleries/technologies/radiology.html.