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phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
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change confusing variable names in preprocessing routines #8

Closed phbradley closed 2 years ago

phbradley commented 3 years ago

The arguments to conga.preprocess.filter_normalize_and_hvg are not as clear as they could be (I don't even remember where they came from originally, probably borrowed from some scanpy demo). I would like at the very least to change n_genes to max_genes or max_genes_per_cell, and take a closer look at the others as well.

This will require updating the python code as well as any jupyter notebooks.

phbradley commented 2 years ago

Updated conga.preprocess to improve things a bit.