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:
- The path to the input h5ad file containing unfiltered data.
- 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 maintainer
Metadata
1 maintainer
Release files for cell-filter 0.1.2
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| cell_filter-0.1.2.tar.gz | 11.2 kB | Without provenance | Details for cell_filter-0.1.2.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| cell_filter-0.1.2-py3-none-any.whl | Python 3 | none | any | Details for cell_filter-0.1.2-py3-none-any.whl |
Total release size: 23.3 kB
Release files / cell_filter-0.1.2.tar.gz
| Download URL | cell_filter-0.1.2.tar.gz |
|---|---|
| Size | 11.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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uv/0.7.21
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Release files / cell_filter-0.1.2-py3-none-any.whl
| Download URL | cell_filter-0.1.2-py3-none-any.whl |
|---|---|
| Size | 12.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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uv/0.7.21
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Security for cell-filter 0.1.2
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