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The UCSC Xena platform for public and private cancer genomics data visualization and interpretation

Mary Goldman, Brian Craft, Mim Hastie, Kristupas Repečka, Akhil Kamath, Fran McDade, Dave Rogers, View ORCID ProfileAngela N. Brooks, Jingchun Zhu, David Haussler
doi: https://doi.org/10.1101/326470
Mary Goldman
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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Brian Craft
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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Mim Hastie
2Clever Canary, New York, NY, USA
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Kristupas Repečka
3Vilnius University, Vilnius, Lithuania
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Akhil Kamath
4Birla Institute of Technology and Science, Goa, India
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Fran McDade
2Clever Canary, New York, NY, USA
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Dave Rogers
2Clever Canary, New York, NY, USA
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Angela N. Brooks
5Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
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  • ORCID record for Angela N. Brooks
Jingchun Zhu
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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David Haussler
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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Abstract

UCSC Xena is a visual exploration resource for both public and private omics data, supported through the web-based Xena Browser and multiple turn-key Xena Hubs. This unique archecture allows researchers to view their own data securely, using private Xena Hubs, simultaneously visualizing large public cancer genomics datasets, including TCGA and the GDC. Data integration occurs only within the Xena Browser, keeping private data private. Xena supports virtually any functional genomics data, including SNVs, INDELs, large structural variants, CNV, expression, DNA methylation, ATAC-seq signals, and phenotypic annotations. Browser features include the Visual Spreadsheet, survival analyses, powerful filtering and subgrouping, statistical analyses, genomic signatures, and bookmarks. Xena differentiates itself from other genomics tools, including its predecessor, the UCSC Cancer Genomics Browser, by its ability to easily and securely view public and private data, its high performance, its broad data type support, and many unique features.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 05, 2019.
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The UCSC Xena platform for public and private cancer genomics data visualization and interpretation
Mary Goldman, Brian Craft, Mim Hastie, Kristupas Repečka, Akhil Kamath, Fran McDade, Dave Rogers, Angela N. Brooks, Jingchun Zhu, David Haussler
bioRxiv 326470; doi: https://doi.org/10.1101/326470
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The UCSC Xena platform for public and private cancer genomics data visualization and interpretation
Mary Goldman, Brian Craft, Mim Hastie, Kristupas Repečka, Akhil Kamath, Fran McDade, Dave Rogers, Angela N. Brooks, Jingchun Zhu, David Haussler
bioRxiv 326470; doi: https://doi.org/10.1101/326470

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