Scientific Software

UCSC Xena (http://xena.ucsc.edu (link is external)) is a web-based, visual exploration tool for all modes of multi-omic data and associated annotations. Xena has several seminal cancer datasets pre-loaded and ready for visualization including TCGA, ICGC, GTEx and more. The Xena public datasets include somatic SNPs, INDELs, large structural variants, CNV, gene-, transcript-, exon- protein-, miRNA-expression, DNA methylation, phenotypes, and clinical data. Xena dynamically generates KM plots as well as visualizes data in a spreadsheet-like view, box plot, bar graph or scatter plot. Using the data hubs and browser, one can easily view their annotations on top of the Xena datasets, like TCGA, as well as their own genomics data. UCSC Xena fully supports human cells, samples, cell lines, organoids, xenografts, etc, and also has basic support for mouse and other species. Xena Public Data Hubs Access over 200 normalized, public datasets. A collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded."