@article {1532781,
	title = {A user guide for the online exploration and visualization of PCAWG data},
	journal = {Nat Commun},
	volume = {11},
	number = {1},
	year = {2020},
	month = {2020 07 07},
	pages = {3400},
	abstract = {The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user{\textquoteright}s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.},
	keywords = {Chromothripsis, Computational Biology, Data Analysis, Databases, Genetic, Genome, Human, Genomics, Humans, Internet, Mutation, Neoplasms, Software, User-Computer Interface, Whole Genome Sequencing},
	issn = {2041-1723},
	doi = {10.1038/s41467-020-16785-6},
	author = {Goldman, Mary J* and Zhang, Junjun* and Fonseca, Nuno A* and <b>Cort{\'e}s-Ciriano, Isidro*</b> and Xiang, Qian and Craft, Brian and Pi{\~n}eiro-Y{\'a}{\~n}ez, Elena and O{\textquoteright}Connor, Brian D and Bazant, Wojciech and Barrera, Elisabet and Mu{\~n}oz-Pomer, Alfonso and Petryszak, Robert and F{\"u}llgrabe, Anja and Al-Shahrour, Fatima and Keays, Maria and Haussler, David and Weinstein, John N and Huber, Wolfgang and Valencia, Alfonso and <b>Park, Peter J</b> and Papatheodorou, Irene and Zhu, Jingchun and Ferretti, Vincent and Vazquez, Miguel}
}
