cell-filter

A python implementation of the EmptyDrops algorithm.

This is an implementation following the CellRanger/STARSolo algorithm which only evaluates candidate droplets within a specific band of the UMI total distribution (under the knee until a minimum UMI threshold).

Installation

cell-filter is distributed using uv

# Install cell-filter
uv tool install cell-filter

# Check installation
cell-filter --help

Usage

To run cell-filter with default parameters you'll need two arguments:

1. The path to the input h5ad file containing unfiltered data.
2. The path to the write the output h5ad file containing filtered data.

cell-filter <input.h5ad> <output.h5ad>

Feel free to explore the code and adjust the parameters to suit your needs.

References

1. EmptyDrops
2. STARsolo
3. CellRanger
4. Good-Turing frequency estimation without tears