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

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Version 2 2023-12-14, 13:27
Version 1 2023-11-29, 18:07
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posted on 2023-12-14, 13:27 authored by Marouen Ben Guebila, Tian Wang, Camila M. Lopes-Ramos, Viola Fanfani, Des Weighill, Daniel Schlauch, Joseph N. Paulson, Michael Altenbuchinger, Katherine H Shutta, Abhijeet R. Sonawane, James Lim, Genis Calderer, David G. P. van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Rebekka BurkholzRebekka Burkholz
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.

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Preferred Citation

Guebila Ben, Tian Wang, Camila Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph Paulson, Michael Altenbuchinger, Katherine Shutta, Abhijeet Sonawane, James Lim, Genis Calderer, IJzendoorn van, Daniel Morgan, Alessandro Marin, Cho-Yi Chen and Qi Song. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. In: Genome Biology. 2023.

Primary Research Area

  • Trustworthy Information Processing

Legacy Posted Date

2023-03-14

Journal

Genome Biology

Open Access Type

  • Green

BibTeX

@article{cispa_all_3910, title = "The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks", author = "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", journal="{Genome Biology}", year="2023", }

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