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bioRxiv · 10.1101/2023.04.21.537695

hipFG: High-throughput harmonization and integration pipeline for functional genomics data

Cifello, J.·Kuksa, P. P.·Saravanan, N.·Valladares, O.·Leung, Y. Y.·Wang, L.-S.
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Abstract

SummaryPreparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG, an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g., chromatin interactions, genomic intervals, quantitative trait loci). Availability and ImplementationhipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. Docker container is available at https://hub.docker.com/r/wanglab/hipfg. Contactlswang@pennmedicine.upenn.edu Supplementary informationSupplementary data are available as BioRxiv supplemental files.

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Cifello, J., Kuksa, P. P., Saravanan, N., Valladares, O., Leung, Y. Y., Wang, L.-S.. 2023-04-25. hipFG: High-throughput harmonization and integration pipeline for functional genomics data. https://doi.org/10.1101/2023.04.21.537695

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