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menchelab / Perturbome

Code to reproduce the study: Mapping the perturbome network of cellular perturbations.
MIT License
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Thanks for the resource! Could you add the All_Vectors_Combined.csv to your github? #1

Open connersk opened 4 years ago

connersk commented 4 years ago

Hi, I'm a PhD student and I enjoyed reading your paper! I'm starting up a project that will also use high throughput imaging to measure the effects of a large small molecule library and I really liked your computational approach for quantifying the morphology of your single drug perturbations and thought that its super cool how target similarity on the interactome relates to morphological similarity (i.e. Figure 3 of your paper).

I'd love rerun your pipeline for calculating the morphological space so that I can get a better sense of how it works and see if I can incorporate it into my work, but unfortunately the ipynb file 8_Validate_Morphospace.ipynb references another file data/Validate_Morphospace/All_Vectors_Combined.csv that I can't find on the github. Would it be possible to add the All_Vectors_Combined.csv file to the github? I'd really appreciate it!

Best, Conner Kummerlowe

mcaldera commented 4 years ago

Dear Conner,

I'm glad you liked our study and our approach to relate interactome distance and cellular morphology. Indeed your are right, the All_Vectors_Combined.csv hasn't been uploaded. I tried to upload it now manually and figured out that the reason for it seems to be file size (apparently 68mb is too large for Github).

For the future we will try to include a script to Github that automatically downloads the missing file(s) but for now please use the following link: https://drive.google.com/open?id=1cJ7odhqIPWhjzMykKfOix4-heQ7Lv5T6

Hope it works now, else please let us know!

All the best, Michael

connersk commented 4 years ago

Thanks, appreciate it!