Extend methods in `phenoscore` and `phenostats` modules - Githubissues

ArcInstitute / ScreenPro2

Flexible analysis of high-content CRISPR screening

https://screenpro2.rtfd.io

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Extend methods in `phenoscore` and `phenostats` modules #12

Open abearab opened 6 months ago

abearab commented 6 months ago

[ ] #4

phenoscore

[x] #25
[ ] Implement ScreenProcessing's stats for libraries with multiple sgRNA elements per target
[ ] #71
[ ] Write function to run robust ranking aggregation (RRA) algorithm
[ ] #72
[ ] #73

phenostats

[x] #11
[x] #34
[x] Implement simple stats.ttest_ind test
- https://github.com/scipy/scipy/issues/18069
[ ] Implement Kolmorogov-Smirnov test

related papers / tools / scripts:

Reproducibility metrics for CRISPR screens | bioRxiv | Cell Systems
Fudging the volcano-plot without dredging the data https://www.nature.com/articles/s41467-024-45834-7
CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves https://www.nature.com/articles/s41467-023-43696-z
- https://github.com/kusterlab/curve_curator
  
  root – https://github.com/GilbertLabUCSF/ScreenPro2/issues/19

abearab commented 5 months ago

Nick

Why average among replicates instead of including that technical variance in the model?

Abe

How would you do that? Any examples?

Nick

Use a model that allows for intra-sample variation (e.g., a linear mixed model or other hierarchical model).