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An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks

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Fig. 1: Netbooks contains a catalog of 19 case studies in regulatory genomics using the Network Zoo tools.

Code availability

Netbooks can be accessed through http://netbooks.networkmedicine.org and the individual Jupyter notebooks are available at https://github.com/netZoo/netbooks.

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Acknowledgements

M.L.K. and R.T.P. are supported by grants from the Norwegian Research Council (313932) and the Norwegian Cancer Society (214871). M.L.K. is also supported by the Norwegian Research Council, Helse Sør-Øst and University of Oslo through the Centre for Molecular Medicine Norway (187615). K.G. is supported by a grant from the US National Heart, Lung, and Blood Institute, National Institutes of Health, K25HL133599. J.P. is supported by US National Heart, Lung, and Blood Institute grant K25HL140186. C.M.L.-R., R.B., D.W., M.B.G. and J.Q. are supported by a grant from the National Cancer Institute, National Institutes of Health, R35CA220523; J.Q. and M.B.G. are also supported by U24CA231846; J.Q. is supported by additional grants from the US National Institutes of Health, 2P50CA127003, 5R01CA205406 and 5R01HL135142. C.M.L.-R. is also supported by a grant from the American Lung Association, LCD-821824 and by the National Heart, Lung, and Blood Institute, 5T32HL007427-41. M.F. is supported by a Marie Sklodowska-Curie grant (PATTERNS 845083). M.A. is supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant no. 01ZX1912C).

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M.B.G. and J.Q conceived the project. D.W., C.M.L.-R, R.B., R.T.P., K.P., M.S., M.F., D.S., K.G., M.A., M.L.K. and J.P. contributed use cases for the collection of notebooks. All authors edited and approved the final manuscript.

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Correspondence to John Quackenbush.

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The authors declare no competing interests.

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Nature Methods thanks Laurence Calzone and Michael Reich for their contribution to the peer review of this work.

Supplementary Information

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Supplementary Note 1 and Table 1

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Ben Guebila, M., Weighill, D., Lopes-Ramos, C.M. et al. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods 19, 511–513 (2022). https://doi.org/10.1038/s41592-022-01479-2

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