Metadata-Version: 2.1
Name: sincei
Version: 0.4
Summary: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data 
Project-URL: Documentation, https://sincei.readthedocs.io/
Project-URL: Source, https://github.com/vivekbhr/sincei
Project-URL: Home-page, https://github.com/vivekbhr/sincei
Author: Vivek Bhardwaj
Maintainer-email: Vivek Bhardwaj <v.bhardwaj@uu.nl>
License: MIT license:
        
        Copyright 2021 Vivek Bhardwaj
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
License-File: LICENCE.txt
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown


<img align="right" src="./docs/content/images/sincei-logo.png">


## sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.

[![DOI](https://zenodo.org/badge/271841139.svg)](https://zenodo.org/badge/latestdoi/271841139) [![Documentation Status](https://readthedocs.org/projects/sincei/badge/?version=latest)](https://sincei.readthedocs.io/en/latest/?badge=latest) [![PyPI Version](https://img.shields.io/pypi/v/sincei.svg?style=plastic)](https://pypi.org/project/sincei/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![test](https://github.com/vivekbhr/sincei/actions/workflows/test.yml/badge.svg)](https://github.com/vivekbhr/sincei/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/vivekbhr/sincei/graph/badge.svg?token=VRTMITHHBI)](https://codecov.io/gh/vivekbhr/sincei)

## Features

sincei provides a flexible, easy-to-use command-line interface to work with single-cell data directly from BAM files. It can:

 - Aggregate signal in bins, genes or any feature of interest from single-cells.
 - Perform read-level and count-level quality control.
 - Perform dimentionality reduction and clustering of all kinds of single-cell data (open chromatin, histone marks, methylation, gene expression etc..).
 - Create coverage files (bigwigs) for visualization.

## [Full Documentation](http://sincei.rtfd.io/)

Please browse the full documentation for tutorials on how to use sincei on command line, as well as details of our python API.

## Installation

sincei is a command line toolkit based on python3, and can be installed using [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).

Create a new conda environment and install sincei stable release from github using:

```
conda create -n sincei -c anaconda python=3.8
conda activate sincei
(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@master#egg=sincei
```

For the development version, try:

```
(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@develop#egg=sincei
```

## Usage

**Get the tool list with `sincei --help`**

Each tool begins with the prefix sc<tool_name>, such as:

```
scBulkCoverage -b file1.bam -g groupinfo.txt -o coverage
```

## Questions and discussions

To ask  a question related to sincei or start a new discussion, please use our [github discussion forum](https://github.com/vivekbhr/sincei/discussions).
