RT Journal Article
SR Electronic
T1 Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 865295
DO 10.1101/865295
A1 Jayaram Kancherla
A1 Yifan Yang
A1 Hyeyun Chae
A1 Hector Corrada Bravo
YR 2019
UL http://biorxiv.org/content/early/2019/12/05/865295.abstract
AB 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.