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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 and the individual Jupyter notebooks are available at


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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.

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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).

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