This repository contains all supporting analyses and files for Ramezani, Bauman, Singh, and Weisbart, et al. "A genome-wide atlas of human cell morphology".
@calvinjan I'm going to go ahead and merge this into main. Please take a close look at your convenience.
I did have to make several minor changes to get what you sent me to run, including a couple guesses at what was intended. The waterfall plot looks the same as your notebook but the GSEA bar graph is a bit different. (This will be run one more time before we call it final, but please let me know if it is problematic if this is what the final result looks like.)
Notable changes:
to make the query_np work in the spatial.distance.cosine I had to .ravel() it to make it 1-D.
res did not have a column named fdr so I guessed you meant NES
@calvinjan I'm going to go ahead and merge this into main. Please take a close look at your convenience. I did have to make several minor changes to get what you sent me to run, including a couple guesses at what was intended. The waterfall plot looks the same as your notebook but the GSEA bar graph is a bit different. (This will be run one more time before we call it final, but please let me know if it is problematic if this is what the final result looks like.)
Notable changes:
query_npwork in thespatial.distance.cosineI had to.ravel()it to make it 1-D.resdid not have a column namedfdrso I guessed you meantNES