CrossMP

CrossMP is a Python-based deep learning model designed to translation between scRAN-seq and scATAC-seq.

Installation

Install CrossMP environment using conda:

conda env create -f environment_crossmp.yml
conda activate crossmp

Usage

Preprocess

Preprocess the scATAC-seq and scRNA-seq data by running:

python preprocess/preprocessing.py --atac ATAC.h5ad --rna RNA.h5ad --organism human --outdir output_dir

Generating the gene activity scores after completing the scATAC-seq preprocessing:

Rscript preprocess/GeneActivityScore.R  output_dir

Preprocess the gene activity scores by running:

python preprocess/preprocessing_rp.py --organism human --datadir output_dir 

Train & evaluate model

conda activate crossmp
python train.py  --outdir model_out --datadir data_dir

Note that the data_dir is the output_dir used during preprocessing.