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Updated: Jul 11, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

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

Jeffrey Cifello¹, Pavel P Kuksa¹, Naveensri Saravanan¹

¹Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.

Bioinformatics (Oxford, England)

|November 10, 2023

Summary

This summary is machine-generated.

Functional genomic (FG) data integration is challenging. The hipFG pipeline automates normalization of diverse FG data, creating standardized, searchable datasets for analysis.

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Last Updated: Jul 11, 2025

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Area of Science:

Genomics
Bioinformatics

Background:

Preparing diverse functional genomic (FG) data for analysis is a complex and time-consuming task.
Integrating heterogeneous FG data types (e.g., chromatin interactions, genomic intervals, quantitative trait loci) into analysis workflows presents significant challenges.

Purpose of the Study:

To introduce hipFG (Harmonization and Integration Pipeline for Functional Genomics), a novel automated pipeline.
To enable efficient and scalable normalization of heterogeneous FG data collections.

Main Methods:

hipFG automatically customizes a pipeline for data normalization.
The pipeline standardizes, indexes, and prepares FG data for rapid searching and analysis.
It accounts for various FG datatypes.

Main Results:

hipFG transforms heterogeneous FG data into analysis-ready datasets.
The pipeline ensures data standardization and efficient searchability.
Scalable normalization of large FG data collections is achieved.

Conclusions:

hipFG addresses the challenge of functional genomic data integration.
The pipeline facilitates efficient analysis of diverse genomic datasets.
hipFG provides a standardized and searchable solution for functional genomics research.