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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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Estimating cell-type fractions from bulk RNA #62

Closed danieljrichard closed 1 year ago

danieljrichard commented 1 year ago

Hello, I've run Ecotyper discovery to define new cell-states for a set of seven different cell types in an scRNA-seq dataset. Now I've run the cell-type recovery (Tutorial 1) on ~50 bulk RNA samples, and have estimated cell-state abundances for each cell type per-sample. However, I'm wondering if there's a way to define the fraction of cell-types for a given bulk sample, similar to what would be output with something like CIBERSORTX. Like sample1 has 40% of cell type 1 (of which, 20% is state 1, 30% state2, etc.), 60 % of cell type 2 (etc.)

Looking through the source code, I have a rough idea how the cell-state abundances are calculated using the NMF data, but am not sure if this math is appropriate for cell-fraction estimation.

Thanks,

Daniel Richard

BALuca commented 1 year ago

Hi Daniel,

EcoTyper does not support the direct estimation of cell type abundances in bulk data at the recovery stage. For this task, you would need to use CIBERSORTx or similar methods. I hope it helps.

Best, The EcoTyper team