{"repo":"slowkow/harmonypy","free":true,"listed":false,"github":"https://github.com/slowkow/harmonypy","clone":"git clone https://github.com/slowkow/harmonypy.git","description":"🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.","language":"Python","stars":280,"topics":["data-science","data-integration","bioinformatics","single-cell-analysis"],"license":"GPL-3.0","category":"data-pipelines","readme_excerpt":"harmonypy [![PyPI][pb]][pypi] [![Downloads][db]][pypi] [![Tests][gb]][yml] [![DOI][zb]][zen] [pb]: https://img.shields.io/pypi/v/harmonypy.svg [pypi]: https://pypi.org/project/harmonypy/ [db]: https://img.shields.io/pypi/dm/harmonypy?label=downloads [gb]: https://github.com/slowkow/harmonypy/actions/workflows/python-package.yml/badge.svg [yml]: https://github.com/slowkow/harmonypy/actions/workflows/python-package.yml [zb]: https://img.shields.io/badge/DOI-10.5281/zenodo.4531400-blue [zen]: https://doi.org/10.5281/zenodo.4531400 harmonypy is a Python package for the [Harmony] algorithm for integrating multiple high-dimensional datasets. It uses a C++ backend (Armadillo) for fast linear algebra, matching the [R harmony2 package][Harmony] step-by-step. This animation shows Harmony aligning three single-cell RNA-seq datasets from different donors. → How to make this animation. Before Harmony, you can clearly distinguish cells from each of the three donors. After Harmony, the cells from different donors are mixed while preserving the overall shape of the data. Installation Install from PyPI (pre-built wheels for Linux and macOS): Building from source Building from source requires a C++ compiler, CMake, and a BLAS library: macOS (uses Apple Accelerate, no extra dependencies): Linux (requires OpenBLAS): Quick Start Usage with Scanpy Parameters run harmony accepts the same parameters as the R package: Parameter Default Description ----------- --------- ------------- theta 2 Diversity","default_branch":null,"files":null,"tree":[],"storefront":"/r/slowkow","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/slowkow/harmonypy/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}