Metadata-Version: 2.4
Name: sincei
Version: 0.5
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>, Fernando Sancho Gómez <f.sanchogomez@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.

 [![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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sincei/README.html)

## 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 dimensionality reduction and clustering of all kinds of single-cell data (open chromatin, histone marks, methylation, gene expression etc..).
 - Create coverage files (bigwigs) for visualization.

For details, please [**read our preprint**](https://www.biorxiv.org/content/10.1101/2024.07.27.605424v1) describing sincei.

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

Please browse the full documentation for tutorials on how to use sincei on the 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).

The recommended way to install sincei is via bioconda:

```
conda create -n sincei -c bioconda -c conda-forge sincei
```

Alternatively, a development version can be installed via GitHub.

```
conda create -n sincei python=3.8
conda activate sincei
pip install --editable=git+https://github.com/bhardwaj-lab/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
```

## Citation

Please cite sincei as: "Bhardwaj V. , Mourragui, S. (2024) User-friendly exploration of epigenomic data in single cells using sincei. biorXiv. [doi: 10.1101/2024.07.27.605424](https://www.biorxiv.org/content/10.1101/2024.07.27.605424v1.full)"

## 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).
