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atakanekiz / CIPR-Package

Cluster Identity Predictor (R package implementation)
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Combining ref dataset by harmonization #7

Open akhst7 opened 2 years ago

akhst7 commented 2 years ago

HI,

In Single R, LTLA describes the way to combine two or more ref data sets (eg. Immgen and Bluecode) by harmonization, which differs from a simple combination of ref data set by c(ref1, ref2). I'd like to combine a custom ref. data (from pubic scRNAseq data of mouse skin) and the immune ref dataset. The custom ref. dataset created by mouse skin RNAseq data very much lack immune cell profiles while Immgen lacks detailed dermal cell profiles. is it possible to implement ref dataset harmonization om CIPR ?

atakanekiz commented 2 years ago

Hello,

Sorry, I just saw this. What you suggest would be a pretty good feature, but for that, I suspect different datasets should be normalized the same way (cpm maybe?). I will look into this but it is difficult to promise a quick turnaround. In the meantime, may I suggest creating stitched cpm-normalized data frames and providing these as a custom reference?