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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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MAGIC and batches #199

Open AVitriolo opened 2 years ago

AVitriolo commented 2 years ago

Ciao,

I am currently using MAGIC before integration/batch correction but -for many reasons - I am now considering modifying a bit your work, to inform MAGIC with an alternative PCA or set of distances, specifically generated after batch(etc)-correction. I'm not considering modifying count values in the input at the moment. Since it's not described explicitly here, and I have not even started to seriously delve into the code, I was wondering if this possibility is already there as an easter-egg, or if you are already working on this.

LiuCanidk commented 1 month ago

Hi there, I have the same idea on the batch integration and wonder if I can input the embedding of batch effect removal, e.g., harmony embedding, to the magic function, is there any progress? or should I perform magic over each individual sample and then merge them? Thanks in advance