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A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

Project description

NS-Forest

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 to get started.

Versioning and citations

This is version 3.9.1. Earlier releases are managed in 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

License

This project is licensed under the MIT License.

Acknowledgments

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

Project details


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Source Distribution

nsforest-3.9.2.3.tar.gz (5.5 kB view hashes)

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Built Distribution

nsforest-3.9.2.3-py3-none-any.whl (6.1 kB view hashes)

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