https://github.com/allencellmodeling/elastic_net_gene_selection

scRNA-seq gene selection code
https://github.com/allencellmodeling/elastic_net_gene_selection

Last synced: 3 months ago
JSON representation

scRNA-seq gene selection code

• Host: GitHub
• URL: https://github.com/allencellmodeling/elastic_net_gene_selection
• Owner: AllenCellModeling
• License: other
• Created: 2020-06-17T19:22:10.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-09-24T22:18:19.000Z (over 4 years ago)
• Last Synced: 2025-01-02T23:14:21.810Z (5 months ago)
• Language: Python
• Homepage:
• Size: 5.73 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
# Elastic Net Gene Selection

[![Build Status](https://github.com/AllenCellModeling/elastic_net_gene_selection/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/elastic_net_gene_selection/actions)

[![Documentation](https://github.com/AllenCellModeling/elastic_net_gene_selection/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/elastic_net_gene_selection)

[![Code Coverage](https://codecov.io/gh/AllenCellModeling/elastic_net_gene_selection/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/elastic_net_gene_selection)

scRNA-seq gene selection code

---

## Installation

First create a conda environment with

```

conda create -n enetgsel python=3.8

conda activate enetgsel

conda install -c conda-forge fortran-compiler

```

Then:

**Stable Release:** `pip install elastic_net_gene_selection`


**Development Head:** `pip install git+https://github.com/AllenCellModeling/elastic_net_gene_selection.git`

## Documentation

For full package documentation please visit [AllenCellModeling.github.io/elastic_net_gene_selection](https://AllenCellModeling.github.io/elastic_net_gene_selection).

## Development

See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.

## The Four Commands You Need To Know

1. `pip install -e .[dev]`

    This will install your package in editable mode with all the required development

    dependencies (i.e. `tox`).

2. `make build`

    This will run `tox` which will run all your tests in both Python 3.6, Python 3.7,

    and Python 3.8 as well as linting your code.

3. `make clean`

    This will clean up various Python and build generated files so that you can ensure

    that you are working in a clean environment.

4. `make docs`

    This will generate and launch a web browser to view the most up-to-date

    documentation for your Python package.

## TODO: Additional Optional Setup Steps:

* Register your project with PyPI:

  * Make an account on [pypi.org](https://pypi.org)

  * Go to your [GitHub repository's settings and under the `Secrets` tab](https://github.com/AllenCellModeling/elastic_net_gene_selection/settings/secrets),

  add a secret called `PYPI_TOKEN` with your password for your PyPI account.

  Don't worry, no one will see this password because it will be encrypted.

  * Next time you push to the branch: `stable`, GitHub actions will build and deploy

  your Python package to PyPI.

  * _Recommendation: Prior to pushing to `stable` it is recommended to install and run

  `bumpversion` as this will,

  tag a git commit for release and update the `setup.py` version number._

***Free software: Allen Institute Software License***