Metadata-Version: 2.1
Name: nsforest
Version: 3.9.2.3
Summary: A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
License: MIT
Author: Renee Zhang
Author-email: zhangy@jcvi.org
Maintainer: Tian Liu
Maintainer-email: ttl074@ucsd.edu
Requires-Python: >=3.8,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: scanpy (>=1.9.3,<2.0.0)
Description-Content-Type: text/markdown

# NS-Forest

<img src="NS-Forest-sticker.png" width="110" height="125">

## Getting Started

Download NSForest_v3dot9_1.py.

### Prerequisites

* This is a python script written and tested in python 3.8, scanpy 1.8.2, anndata 0.8.0.
* Other required libraries: numpy, pandas, sklearn, itertools, time, tqdm.

### Tutorial

Follow the [tutorial](https://jcventerinstitute.github.io/celligrate/tutorials/NS-Forest_tutorial.html) to get started.

## Versioning and citations

This is version 3.9.1. Earlier releases are managed in [Releases](https://github.com/JCVenterInstitute/NSForest/releases).  

Version 2 and beyond:

Aevermann BD, Zhang Y, Novotny M, Keshk M, Bakken TE, Miller JA, Hodge RD, Lelieveldt B, Lein ES, Scheuermann RH. A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing. Genome Res. 2021 Jun 4:gr.275569.121. doi: 10.1101/gr.275569.121.

Version 1.3/1.0:

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH. Cell type discovery using single-cell transcriptomics: implications for ontological representation. Hum Mol Genet. 2018 May 1;27(R1):R40-R47. doi: 10.1093/hmg/ddy100.

## Authors

* Yun (Renee) Zhang zhangy@jcvi.org
* Richard Scheuermann RScheuermann@jcvi.org
* Brian Aevermann baevermann@chanzuckerberg.com


## License

This project is licensed under the [MIT License](https://github.com/JCVenterInstitute/NSForest/blob/master/LICENSE).

## Acknowledgments

* BICCN
* Allen Institute of Brain Science
* Chan Zuckerberg Initiative
* California Institute for Regenerative Medicine
