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KChen-lab / METAFlux

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How to convert from python to R #8

Open Fanyu000 opened 5 months ago

Fanyu000 commented 5 months ago

Hi, I have finished scRNA-seq cell annotation in python with standardized pipeline. I only want to compare the metabolism activity between 3 subtypes. I want to know if 1.I should convert the h5ad file to seurat file format, and then follow the scRNA-seq pipeline. 2.Choose the pipeline option with only 1 sample?

Fanyu000 commented 5 months ago

I have completed covert the h5ad to seurat readable file format, and output a glucose uptake table based on my dataset. image And I aslo want to search for other metabolism pathways, such as fatty acid metabolism, should I change these codes

glucose<-data.frame(glucose=flux[grep("HMR_9034",rownames(flux)),]) glucose cbrt <- function(x) { sign(x) * abs(x)^(1/3) } glucose=cbrt(glucose)

to search for the metabolism pathways I'm interasted, then follow the same pipeline to acquire corresponding results?

Thanks :)

LiuCanidk commented 4 months ago

Hi, I think you have already proposed the solution by yourself. Just change the label of different metabolic pathways to see the difference one by one if you already know what you are interested in.