updated citation

README.md

@@ -4,7 +4,7 @@
 
 ## 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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sincei/README.html)
+ [![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
 
@@ -15,6 +15,8 @@ sincei provides a flexible, easy-to-use command-line interface to work with sing
  - 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.
 
+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 command line, as well as details of our python API.
@@ -47,6 +49,10 @@ 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"
+
 ## 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).

docs/index.rst

@@ -4,10 +4,6 @@
       :align: left
       :width: 350
 
-.. image:: https://zenodo.org/badge/271841139.svg
-    :target: https://zenodo.org/badge/latestdoi/271841139
-    :alt: DOI
-
 .. image:: https://readthedocs.org/projects/sincei/badge/?version=latest)]
     :target: https://sincei.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
@@ -20,7 +16,10 @@
     :target: http://bioconda.github.io/recipes/sincei/README.html
     :alt: Install with bioconda
 
-Bhardwaj V. and Mourragui S. (2023) sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.
+sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.
+
+
+sincei is described in our preprint: `Bhardwaj V. , Mourragui, S. (2024) User-friendly exploration of epigenomic data in single cells using sincei. <https://www.biorxiv.org/content/10.1101/2024.07.27.605424v1>`__