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How to carry out cell deconvolution GIVEN known cell proportions already?

I'm finding a lot of deconvolution libraries like (BisqueRNA and CIBERSORT etc.) but all calculate the cell proportions for me before doing further analysis like differential gene expression. Does anyone have a suggested workflow or library that lets me provide known cell proportions for bulk RNA sequencing data.

For additional information:

I have the cell type fractions, mixture data, and the signature data formatted as "Gene,Tumor,Immune,Fibroblast" etc.

deconvolution
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written by Rashid • Rashid

1 answer

For future reference - I ended up doing this from scratch in Python. It's quite easier than I thought.

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written by Rashid • Rashid

If you have code to share that would be very useful. Just saying that you did this does not help future users.

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written by GenoMax GenoMax

I am imputing the datasets using MAGIC for smoothing and then manually doing the math for deconvolution as libraries like Music etc didn't cut it. it's a few formulas - I will release source code soon once I'm done with this pipeline project.

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written by Rashid • Rashid

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