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prabhakarlab / Banksy_py

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Subject: Request for Access to DLPFC Dataset Used in Your Recent Study #5

Closed ZhiWeiZhang0336 closed 6 months ago

ZhiWeiZhang0336 commented 6 months ago

Hello Prabhakarlab, I am writing to express my admiration for your recent work published in Nature Genetics, titled "BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis." Your findings have significantly contributed to our understanding of BANKSY model, and I am particularly interested in how your model performs on various datasets.

I am currently involved in a project where I have a particular interest in your work on the DLPFC dataset. Given the high relevance of your research to my work, I would be extremely grateful if you could share the code used for testing the model on the DLPFC dataset, or provide any resources that could help assess the applicability of the model to similar studies. This would greatly assist us in our comparative analysis.

I understand the challenges and sensitivities associated with sharing data, and I assure you that any shared resources will be used solely for academic purposes with appropriate acknowledgment of your pioneering contributions.

Thank you very much for considering my request. I am looking forward to the possibility of extending the impact of your work through my research.

jleechung commented 6 months ago

Hi @ZhiWeiZhang0336, thanks for your interest in BANKSY. The DLPFC dataset is publicly available here https://research.libd.org/spatialLIBD/, and the corresponding paper here https://www.nature.com/articles/s41593-020-00787-0.

Code for the results presented in the BANKSY paper can be found here https://github.com/jleechung/banksy-zenodo. We also have vignettes describing multi-sample analysis on DLPFC here https://prabhakarlab.github.io/Banksy/articles/multi-sample.html.

vipulsinghal02 commented 6 months ago

Hi @ZhiWeiZhang0336, we are closing the issue for now. Let us know if you have any trouble accessing the data linked above (and reopen this issue if you need to!). By the way, integrative analysis on the DLPFC data can be found here. Also, note that the lambda parameter for Visium v1 and v2 (55um spot size) is 0.2, not 0.8 (see for example any DLPFC vignette or the BANKSY paper).