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Mye-InfoBank / scRAFIKI

A nextflow pipeline for processing sc-RNASeq data, performing QC and integration and preparing the results for further investigation using cellxgene.
BSD 3-Clause "New" or "Revised" License
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Add an additional way of investigating differential expression between clusters #25

Open nictru opened 9 months ago

nictru commented 9 months ago

The DGEA functionality of cellXgene works, but is pretty slow for atlas-sized datasets. It would be great if we could come up with an additional visualization option, giving the experts more flexibility in investigating the expression profiles.

nictru commented 9 months ago

According to this paper and Leon Hafner's experience, pseudobulk analysis should be best suited for our use case.

We could potentially group all cells from the same sample within the same cluster to one pseudo-sample and then use deseq for differential expression analysis

nictru commented 9 months ago

For pseudobulking, this script could be helpful

nictru commented 9 months ago

Also metacells could be interesting

nictru commented 9 months ago

This lost importance, since the performance of cellxgene is way higher since the switch to CSC sparse matrices.