Supplementary 7 - Githubissues

broadinstitute / 2022_PERISCOPE

This repository contains all supporting analyses and files for Ramezani, Bauman, Singh, and Weisbart, et al. "A genome-wide atlas of human cell morphology".

BSD 3-Clause "New" or "Revised" License

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Supplementary 7 #20

Closed ErinWeisbart closed 10 months ago

ErinWeisbart commented 1 year ago

@MarziehHaghighi I'm sorry that I've lost track of where else we were discussing the code you wrote for generating the cell images, but we're hoping to get the paper draft sent to all the authors this week so if you could upload your code to this repo soon, that would be really helpful. It should go into a folder called Supplemental_7. Please let me know if you have any questions. Thanks!

@MerajRamezani also has items to put into the folder so I will make sure to pull PRs as soon as I can after they come in so either of you can get started uploading.

MarziehHaghighi commented 1 year ago

I put the notebook and all the necessary functions into Supplemental_7 folder, sent a pull request and merged it. I generated one sample output which is placed at outputs folder. The script should work standalone without downloading data or using the single cell vis repo. Let me know if anything is missing. Also, you can find the related email thread with some discussions around this topic by searching Document shared with you: "List of genes for single cell images".

ErinWeisbart commented 1 year ago

@MerajRamezani Can you upload:

the panels that you used as an input to the final figure (Marzieh has uploaded 1, can you add the rest)
the final high resolution Supplemental_7 figure

MerajRamezani commented 1 year ago

@ErinWeisbart no problem.

MerajRamezani commented 1 year ago

@ErinWeisbart I only added the the once which i used (one image per gene) but I also have three extra images per gene (each contain 10 cells) which I can also add.