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Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files

View ORCID ProfileJayaram Kancherla, Yifan Yang, Hyeyun Chae, Hector Corrada Bravo
doi: https://doi.org/10.1101/865295
Jayaram Kancherla
1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland
2Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland
3Department of Computer Science, University of Maryland, College Park, Maryland
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  • ORCID record for Jayaram Kancherla
Yifan Yang
3Department of Computer Science, University of Maryland, College Park, Maryland
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Hyeyun Chae
4Biology and Computer Science, Swarthmore College, Swarthmore, Pennsylvania
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Hector Corrada Bravo
1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland
2Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland
3Department of Computer Science, University of Maryland, College Park, Maryland
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  • For correspondence: hcorrada@umd.edu
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Abstract

Genomic data repositories like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Bioconductor’s AnnotationHub and ExperimentHub etc., provide public access to large amounts of genomic data as flat files. Researchers often download a subset of files data from these repositories to perform their data analysis. As these data repositories become larger, researchers often face bottlenecks in their exploratory data analysis. Based on the concepts of a NoDB paradigm, we developed epivizFileServer, a Python library that implements an in-situ data query system for local or remotely hosted indexed genomic files, not only for visualization but also data manipulation. The File Server library decouples data from analysis workflows and provides an abstract interface to define computations independent of the location, format or structure of the file.

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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 4.0 International license.
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Posted December 05, 2019.
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Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files
Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Hector Corrada Bravo
bioRxiv 865295; doi: https://doi.org/10.1101/865295
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Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files
Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Hector Corrada Bravo
bioRxiv 865295; doi: https://doi.org/10.1101/865295

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