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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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Post 22Q2 data inclusion #95

Open j-andrews7 opened 2 months ago

j-andrews7 commented 2 months ago

Are there any plans to include more recent releases? I know they changed the format of their data releases pretty significantly, but there's also been a significant amount of new data added for some disease entities that were not previously well represented.

lgatto commented 2 months ago

Thank you for your interest. Yes, we are working on adding the latest data to the package - tagging @andreavicini who's working on it.

In the meantime, if it's of any help, you can now also access the original data with depmap.

lgatto commented 1 month ago

Hi @j-andrews7 - do you have any experience with the new files. We struggle to match what we did to the new release. We could also add new tables, depending on your needs. Could you help?

j-andrews7 commented 1 month ago

Is the question which files of the new release correspond to the files in the last release included in this package? Or that the format for several of those corresponding tables has changed?

Regardless, I am happy to help, though it may take be a bit to get to it.

lgatto commented 1 month ago

We can identify all the CCLE to Omics correspondances, but it's not clear for the 22Q2 Achilles_metadata.csv file. If you could help with that, that would be great.

But more generally, it might be worth reconsidering what is repackaged in depmap and how. So if you have specific needs or suggestions, these are also welcome.

j-andrews7 commented 1 month ago

Yeah, I will take a look and think about what makes sense.

My initial thought would be to provide functions for the "Primary" files for each release. Though I don't know the utility of some of the new "OmicsProfile" files yet.

For reference, I'm using this package to build a database backing a Shiny app for exploring and visualizing CRISPR screens: https://github.com/j-andrews7/CRISPRball/blob/devel/R/utils_depmap.R#L59

I am more or less replicating the DepMap dashboard in the app with more control over figures and data shown for contextualizing hits from one's own screens.