Metadata-Version: 2.1
Name: socube
Version: 1.1
Summary: A simple python package for doublet detection in scRNA-seq data
Home-page: https://github/GCS-ZHN/socube/
Author: Zhang.H.N
Author-email: zhang.h.n@foxmail.com
License: MIT License
Platform: any
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata (>=0.7.8)
Requires-Dist: matplotlib (>=3.5.0)
Requires-Dist: numpy (>=1.20.1)
Requires-Dist: pandas (>=1.3.4)
Requires-Dist: python-highcharts (>=0.4.2)
Requires-Dist: scanpy (>=1.8.2)
Requires-Dist: scikit-learn (>=1.0.1)
Requires-Dist: scipy (>=1.7.3)
Requires-Dist: tables (<=3.6.1)
Requires-Dist: lapjv (>=1.3.1)
Requires-Dist: torch (>=1.8.1)
Requires-Dist: torchvision (>=0.9.1)
Requires-Dist: tqdm (>=4.62.3)
Requires-Dist: umap-learn (>=0.5.2)

# SoCube
![license](https://img.shields.io/badge/license-MIT%20License-blue.svg)
![python](https://img.shields.io/badge/python->=3.7-success.svg)
![torch](https://img.shields.io/badge/torch->=1.8.1-success.svg)
[![docker](https://img.shields.io/badge/docker-support-success.svg)](https://hub.docker.com/r/gcszhn/socube)
[![pypi](https://github.com/GCS-ZHN/socube/actions/workflows/pypi.yml/badge.svg)](https://pypi.org/project/socube/)
[![pmid](https://img.shields.io/badge/PMID-NOT%20available-red.svg)](https://pubmed.ncbi.nlm.nih.gov/)
<img src="fig/workflow.svg" alt="SoCube Workflow">

## Introduction
SoCube is an end-to-end doublet detection tool with novel feature embedding strategy. [User manual](https://www.gcszhn.top/socube/) is published on this repo's github page.

## Installment
You can just install socube by executing pip command. 
```bash
pip install socube
```
For install detail, please see at [user manual](https://www.gcszhn.top/socube/).
## Usage
The basic usage of socube with gpus is as follows.
```bash
socube -i data/pbmc-1C-dm.h5ad --gpu-ids 0
```
Please visit our [user manual](https://www.gcszhn.top/socube/) for usage detail.

## Help
Any problem, you could create an [issue](https://github.com/GCS-ZHN/socube/issues), we will receive an email sent by github and reply it as soon as possible.
