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

被引：0

作者：

Marouen Ben Guebila

Tian Wang

Camila M. Lopes-Ramos

Viola Fanfani

Des Weighill

Rebekka Burkholz

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

Enakshi Saha

Dawn L. DeMeo

Megha Padi

John Platig

Marieke L. Kuijjer

Kimberly Glass

John Quackenbush

机构：

[1] Harvard T.H. Chan School of Public Health,Department of Biostatistics

[2] Boston College,Present Address: Biology Department

[3] Brigham and Women’s Hospital and Harvard Medical School,Channing Division of Network Medicine

[4] University of North Carolina at Chapel Hill,Present Address: Lineberger Comprehensive Cancer Center

[5] Present Address: CISPA Helmholtz Center for Information Security,Present Address: Genospace

[6] LLC,Department of Biochemistry and Molecular Biology

[7] Pennsylvania State University College of Medicine,Present Address: Department of Medical Bioinformatics

[8] University Medical Center Göttingen,Present Address: Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine

[9] Brigham and Women’s Hospital,Department of Molecular and Cellular Biology

[10] University of Arizona,Present Address: Monoceros Biosystems

[11] LLC,Center for Molecular Medicine Norway, Nordic EMBL Partnership

[12] University of Oslo,Department of Pathology

[13] Leiden University Medical Center,Present Address: Department of Pathology

[14] Stanford University School of Medicine,Present Address: School of Biomedical Sciences

[15] Hong Kong University,Present Address: Computational Biology Department

[16] Expert Analytics AS,Leiden Center for Computational Oncology

[17] Dana-Farber Cancer Institute,undefined

[18] Present Address: Institute of Biomedical Informatics,undefined

[19] National Yang Ming Chiao Tung University,undefined

[20] Carnegie Mellon University,undefined

[21] Leiden University,undefined

来源：

Genome Biology | / 24卷

关键词：

Gene regulation; Multi-omic analysis; Network biology; Open-source software;

D O I：

暂无

中图分类号：

学科分类号：

摘要：

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.

引用

共 50 条

[1] The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Ben Guebila, Marouen
Wang, Tian
Lopes-Ramos, Camila M. M.
Fanfani, Viola
Weighill, Des
Burkholz, Rebekka
Schlauch, Daniel
Paulson, Joseph N. N.
Altenbuchinger, Michael
Shutta, Katherine H. H.
Sonawane, Abhijeet R. R.
Lim, James
Calderer, Genis
van IJzendoorn, David G. P.
Morgan, Daniel
Marin, Alessandro
Chen, Cho-Yi
Song, Qi
Saha, Enakshi
DeMeo, Dawn L. L.
Padi, Megha
Platig, John
Kuijjer, Marieke L. L.
Glass, Kimberly
Quackenbush, John
GENOME BIOLOGY, 2023, 24 (01)
[2] NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference
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Salembier, Philippe
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[3] NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference
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