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Cellformer

An implementation of Cellformer from our publication: Berson et al. "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature"

Installation from source

The lastest source version of Cellformer can be accessed by running the following command:

git clone https://github.com/elo-nsrb/Cellformer.git
cd Cellformer

Requirements

  • Python 3
  • PyTorch (2.0.0)
  • ArchR (R version 4.2.2)
  • Scikit-learn (1.2.2)
  • Asteroid (0.5.2)
  • Pytorch-lightning (2.0.4)
  • comet_ml (3.32.8)

In order to install package dependencies, you will need Anaconda. After installing Anaconda, please run the following command to create two conda environnements with R and Pytorch dependencies:

.\setup.sh

Usage

1. Peak calling and peak matrix creation

To create a peak matrix from single-cell ATAC-seq fragment files, please use the following commands:

conda activate R_env
./createPeakMatrix.sh --path_data ./data/ --input_dir ./scDATA/ --metadata ./data/scATAC_cell_annotations.csv

usage: createDataset -p | --path_data PATH_DATA
                     -i | --input_dir INPUT_DIR
                     -m | --metadata METADATA
                     [ -h | --help]
positional arguments:
-p, --path_data         Path to save the peak Matrix
-i, --input_dir         Directory with single cell arrow files
-m, --metadata          Metadata with cell annotations

optional arguments:
-h, --help              show help message and exit

2. Synthetic dataset generation

Synthetic dataset can be created from snATAC-seq peak matrix in AnnData format with celltype and Sample_num columns in obs(see example in data):

./createDataset.sh -p ../data/ -n 500

usage: createDataset -p | --path_data PATH_DATA
                     -n | --nbSamplesPerCase NBSAMPLESPERCASE
                     [ -f | --matrixfilename MATRIXFILEMANE]
                     [ -h | --help]
positional arguments:
-p, --path_data         Path to directory with the peak matrix
-n, --nbCellsPerCase    Number of synthetic samples per individual

optional arguments:
-h, --help              Show help message and exit
-f, --matrixfilename    Name of peak matrix file, default=adata_peak_matrix.h5

3. Pretrained model inference and bulk deconvolution

We provided the pretrained model used in the manuscript in cellformer. The pretrained model can be used to deconvolute bulk peak matrix by running:

conda activate pytorch_env
./deconvolution --model_path cellformer/ --peak_matrix ./data/CTRL_CAUD_AD.peak_countMatrix.txt

Usage: deconvolution  -p | --model_path MODEL_PATH
                      -m | --peak_matrix PEAK_MATRIX
                      [ -h | --help  ]"
positional arguments:
-p, --model_path        Path to model directory with train.yml
-m, --peak_matrix       Peak matrix to deconvolute

optional arguments:
-h, --help              Show help message and exit

You can find an example of the expected peak matrix format CTRL_CAUD_AD.peak_countMatrix.txt in data.

4. Model training

Cellformer can be trained from scratch using a synthetic dataset and configuration file train.yml (see an example in cellformer) by running:

conda activate pytorch_env
./trainModel.sh --model_path cellformer/

usage: trainModel -p | --model_path MODEL_PATH
                  [ -h | --help]
positional arguments:
-p, --model_path        Path to model directory with train.yml

optional arguments:
-h, --help              Show help message and exit

Please modify the path to the data folder in train.yml.

5. Validation using pseudo single cell ATAC-seq data

Validation of the model can done using pseudobulk data by running:

./validationModel.sh --model_path cellformer/ --peak_matrix ./data/validation_data/aggregated_sc_mixture.csv --groundtruth ./data/validation_data/agg_sc_separate.npz

Usage: validationModel  -p | --model_path MODEL_PATH
                        -m | --peak_matrix PEAK_MATRIX
                        -g | --groundtruth GROUNDTRUTH
                        [ -h | --help  ]
positional arguments:
-p, --model_path        Path to model directory with train.yml
-m, --peak_matrix       Peak matrix to deconvolute
-m, --groundtruth       Ground truth file

optional arguments:
-h, --help              Show help message and exit

Licence

This project is covered under the GNU General Public License v3.0