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PyPairs - A python scRNA-Seq classifier

This is a python-reimplementation of the Pairs algorithm as described by A. Scialdone et. al. (2015). Original Paper available under: <https://doi.org/10.1016/j.ymeth.2015.06.021>

A supervided maschine learning algorithm aiming to classify single cells based on their transcriptomic signal. Initially created to predict cell cycle phase from scRNA-Seq data, this algorithm can be used for various applications.

Build to be fully compatible with Scanpy [Wolf18].

Code available on GitHub.

Core Dependencies

Authors

  • Antonio Scialdone - original algorithm
  • Ron Fechtner - implementation and extension in Python

Release notes

Announcement

Note

Please only use pypairs >= 3.0.9.

Versions

Version 3.0.1 - 3.0.9, Feb 1, 2019

  • Various bug fixes

Version 3.0.0, Jan 18, 2019 - Jan 31, 2019

  • Complete restructuring of the package. Now fully compatiple with scanpy .
  • Added:
    • This documentation
    • Default (oscope) dataset & marker pairs [Leng15]
  • Changed:

Version 2.0.1 - 2.0.6, Nov 22, 2018

  • Minor bug fixes and improvements.

Version 2.0.0, Aug 14, 2018

  • Major restructuring of the package
  • Improved parallel processing
  • New features:

Version 1.0.1 - 1.0.3, Jul 29, 2018

  • Bug fixes and improvements. (Mostly bugs though)
  • Added multi-core processing

Version 1.0.0, Mar 4, 2018

  • Speed and performance improvements.

Version 0.1, Feb 22, 2018

  • Simple python reimplementation of the Pairs algorithm.
  • Included sandbag() and cyclone() algorithms