Integrating result with Scanpy

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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Integrating result with Scanpy #6

Closed justinesjw closed 5 years ago

justinesjw commented 6 years ago

Hello!

From you paper you mention that there's a way to integrate SoupX's result with Seurat and Scanpy.

I noticed that there is a function (createCleanedSeurat.R) for Seurat. is there such function for Scanpy?

Thanks!

justinesjw commented 5 years ago

If anyone is looking for an answer to this problem, i converted the matrix to .mtx using

writeMM(sparse_mat, file="outfile.mtx")

and read into scanpy using

adata = sc.read('outfile.mtx', cache=True).T

constantAmateur commented 5 years ago

The output of SoupX is another sparse matrix, which as you observe can be written out and loaded in any downstream analysis package instead of the uncorrected sparse matrix.