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noamteyssier / crispr_screen

Efficient Differential Expression and Gene Aggregation for CRISPR screens.
https://noamteyssier.github.io/crispr_screen/
MIT License
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Visualisation #134

Closed nangosyah closed 2 months ago

nangosyah commented 5 months ago

Hello,

I'm trying to use this implementation to do some analysis on pooled KO-CRISPR experiment with 10 samples divided in two groups: control and treatment. For each sample I have the amount of guideRNA at T0 and at T12. I want to find which genes are differentially expressed.

Is there a way I can account for time in the model and also visualise the results from the work flow.

Thanks

noamteyssier commented 5 months ago

Hey @nangosyah

Unfortunately I don't have a generalized linear model implemented for crispr_screen where you can account for multiple variables and their interactions.

However, you can perhaps run DESeq2 or edgeR with your specific design for the differential abundance analysis and then use crispr_screen agg to aggregate the p-values at a gene level for the sgRNAs on your chosen contrast.

For visualization you can check out my tool screenviz