Tan, Q.W., Lim, P.K., Chen, Z. et al. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun 14, 986 (2023). https://doi.org/10.1038/s41467-023-36517-w
Marchantia polymorpha gene expression atlas reveals the hierarchy of abiotic stress responses and conservation of diurnal gene expression BioArchive: https://doi.org/10.1101/2021.11.12.468350
Welcome to the repository that contains the code that was used for the analyses in the manuscript. We have collated all the relevant code and put it into google colab where you should be able to run the code with minimal edits. Do drop us a message on Github or through email if you encounter any issues.
Update [07 July 2022]: With [new results]https://www.biorxiv.org/content/10.1101/2021.11.12.468350v2, the colab code has expanded and is not fully compatible with Google colab. Some parts should be run locally. The sections have been organised chronologically as much as possible. Should you get stuck on trying to replicate the analysis, do drop me a message.
Update [04 December 2023]: It has come to our attention that the formula for calculating the R2 during GRN reconstruction is erronous. We have reviewed how the results could be affected using R values. Based on how the analysis was carried out, the results remain valid and unaffected, but it should be noted that the R2 values reported are instead, R values. We apologise for the inconvenience caused. The error has been rectified in the [repository]https://github.com/arendma/GRN_code the code has been adapted from.
Cheers!
Qiao Wen [email]qiaowen.tan@ntu.edu.sg