The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Ben Guebila, Marouen and Wang, Tian and Lopes-Ramos, Camila M. and Fanfani, Viola and Weighill, Des and Burkholz, Rebekka and Schlauch, Daniel and Paulson, Joseph N. and Altenbuchinger, Michael and Shutta, Katherine H and Sonawane, Abhijeet R. and Lim, James and Calderer, Genis and van IJzendoorn, David G. P. and Morgan, Daniel and Marin, Alessandro and Chen, Cho-Yi and Song, Qi and Saha, Enakshi and DeMeo, Dawn L. and Padi, Megha and Platig, John and Kuijjer, Marieke and Glass, Kimberly and Quackenbush, John

(2023) The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.

Genome Biology, 24 (1). ISSN 1474-7596

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Official URL: https://doi.org/10.1186/s13059-023-02877-1

Abstract

Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

Item Type:	Article
Divisions:	Rebekka Burkholz (RB)
Depositing User:	Rebekka Burkholz
Date Deposited:	14 Mar 2023 06:56
Last Modified:	14 Mar 2023 06:56
Primary Research Area:	NRA1: Trustworthy Information Processing
URI:	https://publications.cispa.saarland/id/eprint/3910

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