Dataset Information

HipFG: high-throughput harmonization and integration pipeline for functional genomics data.

ABSTRACT:

Summary

Preparing 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 (Harmonization and Integration Pipeline for Functional Genomics), 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 implementation

hipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. A Docker container is available at https://hub.docker.com/r/wanglab/hipfg.

SUBMITTER: Cifello J

PROVIDER: S-EPMC10660288 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Cifello Jeffrey J Kuksa Pavel P PP Saravanan Naveensri N Valladares Otto O Wang Li-San LS Leung Yuk Yee YY

Bioinformatics (Oxford, England) 20231101 11

<h4>Summary</h4>Preparing 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 (Harmonization and Integration Pipeline for Functional Genomics), an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis ...[more]

PMID: 37947320

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