1. A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
- Author
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John N. Weinstein, Jingchun Zhu, Elena Piñeiro-Yáñez, Vincent Ferreti, Robert Petryszak, Elisabet Barrera, Brian O'Connor, Brian Craft, Anja Füllgrabe, Irene Papatheodorou, Peter J. Park, Nuno A. Fonseca, Fatima Al-Shahrour, Mary Goldman, Junjun Zhang, Wojciech Bazant, Alfonso Munoz, Maria Keays, Wolfgang Huber, Alfonso Valencia, David Haussler, Qian Xiang, Isidro Cortes-Ciriano, and M. Vazquez
- Subjects
Resource (project management) ,Chromothripsis ,Data exploration ,Pan cancer ,Computer science ,Genomics ,Genome ,Data science ,Visualization - Abstract
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project has generated, to our knowledge, the largest whole-genome cancer sequencing resource to date. Here we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper: The ICGC Data Portal, UCSC Xena, Expression Atlas, PCAWG-Scout, and Chromothripsis Explorer. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, as well as demonstrate how the tools can be used together to more deeply understand tumor biology. Together, these tools enable researchers to dynamically query complex genomics data and integrate external information, enabling and enhancing PCAWG data interpretation. More information on these tools and their capabilities is available from The PCAWG Data Portals and Visualizations Page (http://docs.icgc.org/pcawg).
- Published
- 2017
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