HALO: Hierarchical Causal Modeling for Single Cell Multi-Omics Data

arXiv BibTeX

Official code for the paper [HALO: Hierarchical Causal Modeling for Single Cell Multi-Omics Data ]

Please cite us when making use of our code or ideas.

Installation

cd $PROJECT_DIR
conda config --set channel_priority flexible
conda env create -f environment.yml -n halo-env
conda activate halo-env

The Pretrained models and datasets

Models
Datasets

Tutorial Notebook

1. the training tutorial: train_tutorial.ipynb

2. the representation analysis tutorial: tutorial_1_representation.ipynb

3. the gene-peak level analysis tutorial: tutorial_2_gene_peaks.ipynb

4. the granger causal analysis tutorial: tutorial_3_granger.ipynb

5. the chromatin potential tutorial: tutorial_3_Chromatin.ipynb

6. the optimal transport analysis tutorial: tutorial_3_Chromatin.ipynb

License

Attribution-NonCommercial-NoDerivatives 4.0 International

BibTex