Va3DE: Variational 3D Embedding for Single-Cell Hi-C Clustering
To run Va3DE download and install the package:
git clone https://github.com/JinLabBioinfo/Va3DE.git;
cd Va3DE;
pip install .
Then you just need to supply a .scool file and a reference file with cell metadata:
va3de --scool data/pfc.scool --reference data/pfc_ref
You can find a full example here:
We supply a variety of preprocessed scHi-C datasets and metadata in our SCORE package: https://github.com/JinLabBioinfo/SCORE