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.

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

The easiest way to install scHiCExplorer is using BioConda

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

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.

Please visit our complete documentation on readthedocs.