The GDC provides user-friendly and interactive Data Analysis, Visualization, and Exploration (DAVE) Tools supporting gene and variant level analysis that allows researchers to:
The GDC provides interactive tools supporting data analysis, exploration, and visualization.
The GDC provides policies for publishing the results of analyzed data.
GDC variant calling pipelines generate high level data for analysis. Variant calling pipelines are implemented using data processing software and algorithms selected in consultation with the expert genomics community.
Cancer Research Highlights and Publications:
HTSeq had been the default RNA-Seq expression quantification tool since the first GDC data release. The GDC later updated the RNA-Seq alignment and quantification workflow to include STAR Count, which generates stranded counts by default in addition to the existing unstranded counts. During Data Release 32 for gene model updates, the GDC had 1) augmented the existing STAR Count output to include FPKM and FPKM-UQ normalizations; 2) reprocessed all the TCGA data using the latest RNA-Seq workflow with STAR Count. Because both tools use very similar counting strategies, and STAR Count has the advantages in both running time and the additional stranded counts, the GDC removed HTSeq workflow in Data Release 32.
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