Closed justinesjw closed 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
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.
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!