https://github.com/euxhenh/grinch

A library for differential expression and gene set enrichment analysis based on hydra and pydantic.
https://github.com/euxhenh/grinch

clustering differential-expression-analysis gene-set-enrichment marker-genes single-cell single-cell-analysis

Last synced: 2 months ago
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A library for differential expression and gene set enrichment analysis based on hydra and pydantic.

• Host: GitHub
• URL: https://github.com/euxhenh/grinch
• Owner: euxhenh
• License: mit
• Created: 2022-07-17T04:19:09.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-12-15T06:57:22.000Z (over 2 years ago)
• Last Synced: 2023-12-15T07:28:57.096Z (over 2 years ago)
• Topics: clustering, differential-expression-analysis, gene-set-enrichment, marker-genes, single-cell, single-cell-analysis
• Language: Python
• Homepage:
• Size: 318 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

          
.. -*- mode: rst -*-

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.. |PythonVersion| image:: https://img.shields.io/badge/python-3.10-blue

.. _PythonVersion: https://pypi.org/project/scikit-learn/

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.. _CircleCI: https://circleci.com/gh/euxhenh/grinch

.. |Codecov| image:: https://codecov.io/gh/euxhenh/grinch/branch/main/graph/badge.svg?token=P8KNCOKJ69

.. _Codecov: https://codecov.io/gh/euxhenh/grinch

**grinch** is a (under development) Python library for single-cell data

analysis aimed at reducing boilerplate code through the use of workflow

'config' files. This encourages reproducibility, minimizes bugs, and allows

the construction of complex pipelines with zero code written.

The library was originally written to prevent overcrowding project

directories with a myriad jupter notebooks and scripts, and replace them

with short and self-explanatory configs. **grinch** supports many steps of

the single-cell analysis pipeline, from normalization and unsupervised

learning, to gene differential expression and gene set enrichment

analysis.

Architecture

____________

**grinch** uses the `AnnData `_

data format to store data matrices and annotations. It relies on `hydra

`_ for parsing `yaml` config files and

`pydantic `_ for data validation.

Usage

_____

Example configs can be found in the `conf` directory. More docs to come...