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;
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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.
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