semvec/pypi-packages huggingface dataset:
scProject-stable 1.1.2
Transfer learning framework for single cell gene expression analysis in Python
License: MIT

# scProject # 

<img src="https://raw.githubusercontent.com/gofflab/scProject/master/docs/scProject-logo.jpg">

## Overview ##

Transfer learning for gene expression signatures (Python implementation of ProjectR).  
Current version: 1.1.2 ([PYPI](https://pypi.org/project/scProject-stable/))

## Description ##

scProject is a software package that allows biologists to use transfer learning to understand the usage of previously discovered features in genomic datasets. Tools like NNMF allow biologists to find a set of vectors that linearly combine to approximately reconstruct a dataset. These features can have biological meaning as a pathway, cell type, gene program, cell feature, etc.  

scProject leverages scikit-learn’s and scipy’s regression tools to effectively perform a change of basis with the new basis being the features discovered from NNMF or another previous analysis tool. For example, the values in the first column of the pattern matrix are the coefficients of the features to approximate the first sample in the dataset. This analysis allows the user to see the usage of features from a previously examined dataset and see if those same features are utilized in a new dataset. Using UMAP-learn to decrease the dimensionality of the regressed pattern matrix allows the user to visualize the pattern matrix in intuitive and informative ways.  

## Installation ##

scProject package can be installed by the following code:  

```python
pip install scProject-stable
```

Currently, the stable version needs to be imported in Python as:

```python
import scProject
```

It is recommended to install the package and run the code in a virtual environment (venv). Use the code below to create and activate venv:  

```python
python -m venv env
source env/bin/activate
```

## Contents ##

Name          | Link
------------- | -------------
scProject API | https://scproject.readthedocs.io/en/master/contents.html
Regression    | https://scproject.readthedocs.io/en/master/contents.html#module-scProject.rg
Visualization | https://scproject.readthedocs.io/en/master/contents.html#module-scProject.viz
Statistics    | https://scproject.readthedocs.io/en/master/contents.html#module-scProject.stats
Utilities     | https://scproject.readthedocs.io/en/master/contents.html#module-scProject.matcher
Tutorial      | https://scproject.readthedocs.io/en/master/tutorial.html


## Additional Information ##

For more instructions and guidelines, read the [documentation](https://scproject.readthedocs.io/en/master/).  
If you would like to leave a feedback, please contact [cshin12@jhu.edu](mailto:cshin12@jhu.edu).
sparkcraft 0.0.4
SparkCraft
License: MIT
Requires Python: >=3.9,<4.0

# SparkCraft

[![PyPI](https://img.shields.io/pypi/v/sparkcraft.svg)][pypi_]
[![Status](https://img.shields.io/pypi/status/sparkcraft.svg)][status]
[![Python Version](https://img.shields.io/pypi/pyversions/sparkcraft)][python version]
[![License](https://img.shields.io/pypi/l/sparkcraft)][license]

[![Read the documentation at https://sparkcraft.readthedocs.io/](https://img.shields.io/readthedocs/sparkcraft/latest.svg?label=Read%20the%20Docs)][read the docs]
[![Tests](https://github.com/MichaelisTrofficus/sparkcraft/workflows/Tests/badge.svg)][tests]
[![Codecov](https://codecov.io/gh/MichaelisTrofficus/sparkcraft/branch/main/graph/badge.svg)][codecov]

[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)][pre-commit]
[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)][black]

[pypi_]: https://pypi.org/project/sparkcraft/
[status]: https://pypi.org/project/sparkcraft/
[python version]: https://pypi.org/project/sparkcraft
[read the docs]: https://sparkcraft.readthedocs.io/
[tests]: https://github.com/MichaelisTrofficus/sparkcraft/actions?workflow=Tests
[codecov]: https://app.codecov.io/gh/MichaelisTrofficus/sparkcraft
[pre-commit]: https://github.com/pre-commit/pre-commit
[black]: https://github.com/psf/black

## Features

- TODO

## Requirements

- TODO

## Installation

You can install _SparkCraft_ via [pip] from [PyPI]:

```console
$ pip install sparkcraft
```

## Usage

Please see the [Command-line Reference] for details.

## Contributing

Contributions are very welcome.
To learn more, see the [Contributor Guide].

## License

Distributed under the terms of the [MIT license][license],
_SparkCraft_ is free and open source software.

## Issues

If you encounter any problems,
please [file an issue] along with a detailed description.

## Credits

This project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter] template.

[@cjolowicz]: https://github.com/cjolowicz
[pypi]: https://pypi.org/
[hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python
[file an issue]: https://github.com/MichaelisTrofficus/sparkcraft/issues
[pip]: https://pip.pypa.io/

<!-- github-only -->

[license]: https://github.com/MichaelisTrofficus/sparkcraft/blob/main/LICENSE
[contributor guide]: https://github.com/MichaelisTrofficus/sparkcraft/blob/main/CONTRIBUTING.md
[command-line reference]: https://sparkcraft.readthedocs.io/en/latest/usage.html