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jump-cellpainting / cpg0014-jump-adipocyte-data

Data repository for cpg0014-jump-adipocyte
BSD 3-Clause "New" or "Revised" License
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Reprocess profiles using jump-profiling-recipe #2

Open shntnu opened 4 months ago

shntnu commented 4 months ago

We need to reprocess the profiles in this repo, starting from the augmented profiles.

  1. Use the upcoming v0.2.0 of https://github.com/broadinstitute/jump-profiling-recipe to do so.
  2. Processing using both pipelines – the CRISPR/ORF pipelines as well as the Compound pipeline
  3. Evaluate using (mAP-based) phenotypic activity
PaulaLlanos commented 1 month ago

I am starting to work on this using the new recipe version. Regarding the recipes to use, besides the compound recipe, should I use CRISPR or ORF? Do you have any preference? Suganya and I discussed using her documentation for the recipes, then I can provide feedback if necessary

shntnu commented 1 month ago

Please go with ORF

PaulaLlanos commented 1 month ago

I noticed that some of the plates have metadata corresponding to the control.txt platemap. This file only includes the well names and an empty column for the condition.

I’m wondering if I should consider this as DMSO, a negative control, or something else. Could you please clarify? thank you!

I've attached a screenshot of the platemap for reference:

Screenshot 2024-10-09 at 11 37 33 AM

shntnu commented 1 month ago

I noticed that some of the plates have metadata corresponding to the control.txt platemap. This file only includes the well names and an empty column for the condition.

I’m wondering if I should consider this as DMSO, a negative control, or something else. Could you please clarify? thank you!

I've attached a screenshot of the platemap for reference:

@jump-cellpainting/broad-claussnitzer can you help address the question above?

Additional info that might help: Here are the platemaps for a single batch; each batch has these control plates (they are different from the Target2 plates)

https://github.com/jump-cellpainting/cpg0014-jump-adipocyte-data/tree/master/metadata/platemaps/2022_11_28_Batch1/platemap

PaulaLlanos commented 1 month ago

Update: I was able to run the ORF jump recipe with some changes that I will document soon, after discuss about it with Suganya and John. I run it considering that empty columns as a 'control' until I get the correct information from @jump-cellpainting/broad-claussnitzer.