BBKNN for ATAC data

[wlason]

Hi! Thank you for the awesome package :) I was wondering if it is possible to use other dimensionality reduction methods than PCA for bbknn.bbknn, such as LSI which is commonly used for ATAC data? use_rep argument would suggest it is possible, but I wanted to check what your thoughts were before running it!

[ktpolanski]

Correct - just point use_rep to whatever you want to use from .obsm.