Dense matrix datasets

Help scanpy
1

Hello,
Single cell datasets are sparse matrix, does Scanpy support dense matrix datasets?

2

Yes it supports either one, to make you data dense:

adata.X = adata.X.toarray()
3

Thanks!
However, I mean is scanpy designed specifically to sparse matrix (single cell data). Now I have some datasets from RNAseq, which are dense matrix. I have imported them into scanpy and run it successfully, such as PCA, umap and so on. I worry that scanpy doesn’t support these techniques (bulk RNAseq).

4

Scanpy is meant to work with both dense and sparse arrays. Some methods (like qc metrics) are likely tested better with sparse arrays, but everything is intended to work with dense or sparse data.