https://github.com/joachimwolff/schicexplorer

Single-cell Hi-C data analysis toolbox
https://github.com/joachimwolff/schicexplorer

bioinformatics hi-c single-cell

Last synced: 3 months ago
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Single-cell Hi-C data analysis toolbox

• Host: GitHub
• URL: https://github.com/joachimwolff/schicexplorer
• Owner: joachimwolff
• License: mit
• Created: 2019-04-17T13:06:04.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2021-08-13T07:23:34.000Z (over 3 years ago)
• Last Synced: 2023-03-03T00:19:24.377Z (almost 2 years ago)
• Topics: bioinformatics, hi-c, single-cell
• Language: Python
• Homepage: https://schicexplorer.readthedocs.io/
• Size: 39.2 MB
• Stars: 10
• Watchers: 1
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
|azure| |rtd| |conda|

.. |azure| image:: https://dev.azure.com/wolffj/scHiCExplorer/_apis/build/status/joachimwolff.scHiCExplorer?branchName=master

	:target: https://dev.azure.com/wolffj/scHiCExplorer/_build/latest?definitionId=1&branchName=master

.. |rtd| image:: https://readthedocs.org/projects/schicexplorer/badge/?version=latest

   :target: http://schicexplorer.readthedocs.io/?badge=latest

.. |conda| image:: https://anaconda.org/bioconda/schicexplorer/badges/installer/conda.svg   

   :target: https://conda.anaconda.org/bioconda

scHiCExplorer

=============

The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data. scHiCExplorer supports the mcool file format and stores per cell one Hi-C interaction matrix in it.

.. image:: ./docs/images/scHi-C_workflow.png

Citation

--------

Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning.

**Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research**, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220

Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn Grüning.

**Scool: a new data storage format for single-cell Hi-C data, Bioinformatics**, Volume 37, Issue 14, 15 July 2021, Pages 2053–2054, https://doi.org/10.1093/bioinformatics/btaa924

Joachim Wolff, Rolf Backofen, Björn Grüning.

**Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs, Bioinformatics**, btab394, https://doi.org/10.1093/bioinformatics/btab394

Availability

------------

The easiest way to install scHiCExplorer is using `BioConda `_

::

   $ conda install schicexplorer -c bioconda -c conda-forge

Install by cloning this repository

__________________________________

You can install any one of the HiCExplorer branches on command line

(linux/mac) by cloning this git repository:

::

    $ git clone https://github.com/joachimwolff/scHiCExplorer.git

    $ cd scHiCExplorer

    $ python setup.py install

However, please take care all dependencies are installed, see the requirements.txt file.

Documentation

-------------

Please visit our complete documentation on `readthedocs `_.