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The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
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 e...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2023
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9999668/ https://www.ncbi.nlm.nih.gov/pubmed/36894939 http://dx.doi.org/10.1186/s13059-023-02877-1 |
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| author | Ben Guebila, Marouen Wang, Tian Lopes-Ramos, Camila M. Fanfani, Viola Weighill, Des Burkholz, Rebekka Schlauch, Daniel Paulson, Joseph N. Altenbuchinger, Michael Shutta, Katherine H. Sonawane, Abhijeet R. Lim, James Calderer, Genis van IJzendoorn, David G.P. Morgan, Daniel Marin, Alessandro Chen, Cho-Yi Song, Qi Saha, Enakshi DeMeo, Dawn L. Padi, Megha Platig, John Kuijjer, Marieke L. Glass, Kimberly Quackenbush, John |
| author_facet | Ben Guebila, Marouen Wang, Tian Lopes-Ramos, Camila M. Fanfani, Viola Weighill, Des Burkholz, Rebekka Schlauch, Daniel Paulson, Joseph N. Altenbuchinger, Michael Shutta, Katherine H. Sonawane, Abhijeet R. Lim, James Calderer, Genis van IJzendoorn, David G.P. Morgan, Daniel Marin, Alessandro Chen, Cho-Yi Song, Qi Saha, Enakshi DeMeo, Dawn L. Padi, Megha Platig, John Kuijjer, Marieke L. Glass, Kimberly Quackenbush, John |
| author_sort | Ben Guebila, Marouen |
| collection | PubMed |
| description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02877-1. |
| format | Online Article Text |
| id | pubmed-9999668 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-99996682023-03-11 The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks Ben Guebila, Marouen Wang, Tian Lopes-Ramos, Camila M. Fanfani, Viola Weighill, Des Burkholz, Rebekka Schlauch, Daniel Paulson, Joseph N. Altenbuchinger, Michael Shutta, Katherine H. Sonawane, Abhijeet R. Lim, James Calderer, Genis van IJzendoorn, David G.P. Morgan, Daniel Marin, Alessandro Chen, Cho-Yi Song, Qi Saha, Enakshi DeMeo, Dawn L. Padi, Megha Platig, John Kuijjer, Marieke L. Glass, Kimberly Quackenbush, John Genome Biol Software 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02877-1. BioMed Central 2023-03-09 /pmc/articles/PMC9999668/ /pubmed/36894939 http://dx.doi.org/10.1186/s13059-023-02877-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
| spellingShingle | Software Ben Guebila, Marouen Wang, Tian Lopes-Ramos, Camila M. Fanfani, Viola Weighill, Des Burkholz, Rebekka Schlauch, Daniel Paulson, Joseph N. Altenbuchinger, Michael Shutta, Katherine H. Sonawane, Abhijeet R. Lim, James Calderer, Genis van IJzendoorn, David G.P. Morgan, Daniel Marin, Alessandro Chen, Cho-Yi Song, Qi Saha, Enakshi DeMeo, Dawn L. Padi, Megha Platig, John Kuijjer, Marieke L. Glass, Kimberly Quackenbush, John The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title | The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title_full | The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title_fullStr | The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title_full_unstemmed | The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title_short | The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| title_sort | network zoo: a multilingual package for the inference and analysis of gene regulatory networks |
| topic | Software |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9999668/ https://www.ncbi.nlm.nih.gov/pubmed/36894939 http://dx.doi.org/10.1186/s13059-023-02877-1 |
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