Input types for count matrix

JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.

https://doubletdetection.readthedocs.io/en/stable/

MIT License

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Input types for count matrix #71

Closed adamgayoso closed 6 years ago

adamgayoso commented 6 years ago

We should at least accept:

Sparse matrices
Pandas DataFrames
10x mtx format

For sparse matrices, we will probably just instantly make them dense.

JonathanShor commented 6 years ago

If it seems worthwhile to fully support sparse in and out, there are some options for getting "around" PCA densifying the matrix, such as a random subsample PCA. I'm not familiar with these approaches, so we'd have to look into them further.

JonathanShor commented 6 years ago

Likely use sklearn.utils.check_array.