Post 22Q2 data inclusion

[j-andrews7]

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]

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]

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]

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]

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]

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.