8000 RCTD for bulk to sc devonvolution · Issue #228 · dmcable/spacexr · GitHub
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RCTD for bulk to sc devonvolution #228
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RCTD for bulk to sc devonvolution#228
@li-xuyang28

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@li-xuyang28
li-xuyang28
opened on Jan 27, 2025

Dear dev team of spacexr,

Thanks for maintaining the package! I am trying to use RCTD to deconvolute TCGA bulkRNAseq with a scRNAseq object as reference (instead of spatial to sc). Our colleague has done this before. However, I noticed one caveat: RCTD prefers to deconvolute based on raw count (which makes sense as it maps to count of scRNAseq). Is it possible to map FPKM from bulk to some sort of pseudo-FPKM of scRNAseq? I was wondering if people have considered this to eliminate any length bias. Thanks!

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