Automated scRNA-seq filtering
Project description
# dropkick Automated cell filtering for single-cell RNA sequencing data.
dropkick works primarily with [Scanpy](https://icb-scanpy.readthedocs-hosted.com/en/stable/)’s AnnData objects, and accepts input files in .h5ad or flat (.csv, .tsv) format. It also writes outputs to .h5ad files when called from the terminal.
— Installation via pip or from source requires a Fortran compiler. For Mac users, brew install gcc will take care of this.
#### Install from PyPI: `bash pip install dropkick `
#### Or compile from source: `bash git clone https://github.com/KenLauLab/dropkick.git cd dropkick python setup.py install `
— dropkick can be run as a command line tool, or interactively with the [scanpy](https://icb-scanpy.readthedocs-hosted.com/en/stable/) single-cell analysis suite.
#### Usage from command line: `bash python -m dropkick path/to/counts.h5ad `
Output will be saved in a new .h5ad file containing __dropkick__ scores, labels, and model parameters.
See [dropkick_tutorial.ipynb](dropkick_tutorial.ipynb) for an interactive walkthrough of the dropkick pipeline and its outputs.
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