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LKremer / scbs

Python package with CLI for the analysis of single cell methylation data. Now known as MethSCAn: https://github.com/anders-biostat/MethSCAn
https://anders-biostat.github.io/MethSCAn/
GNU General Public License v3.0
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Add a method to allow for easy cell filtering (e.g. after QC) #6

Closed LKremer closed 2 years ago

LKremer commented 2 years ago

Currently, you have do this manually by re-running scbs prepare on high-quality cells only. It would be nice if you could just filter low quality or uninteresting cells from DATA_DIR directly.

LKremer commented 2 years ago

I implemented a little filtering utility now, see commit fb62888216495ed72af16f23a1f29c7e6d3600d4. Didn't test this on a big dataset yet. It might be slow since it slices the columns of a sparse matrix optimised for row-wise access. But better than re-running prepare, I guess.

LKremer commented 2 years ago

Tested on ~1000 cells, it's pretty fast.