dropkick 1.1.2

Automated scRNA-seq filtering


### Automated cell filtering for single-cell RNA sequencing data.

[![Latest Version][pypi-image]][pypi-url]

— 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 (brew install gcc for Mac users).

#### 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 dropkick run path/to/counts.h5ad `

Output will be saved in a new .h5ad file containing __dropkick__ scores, labels, and model parameters.

You can also run the dropkick.qc module from terminal for a quick look at the total UMI distribution and ambient genes, saved as *_qc.png: `bash dropkick qc path/to/counts.h5ad `

See [dropkick_tutorial.ipynb](dropkick_tutorial.ipynb) for an interactive walkthrough of the dropkick pipeline and its outputs.

[pypi-image]: https://img.shields.io/pypi/v/dropkick [pypi-url]: https://pypi.python.org/pypi/dropkick/