We upload the conda environment file (It contains the versions of required packages and other information). To install it, please use:

conda env create --name cpsc488 --file=cpsc488_env.yml

To run our codes, please first pre-process the given dataset based on different tasks.

For cell-type annotation task, please use:

python preprocessing_cta.py

For deconvolution task, please use:

python preprocessing_deconv.py

Then for different tasks, we also have different main files.

For cell-type annotation task, please use:

python cta_main.py

For deconvolution task, please use:

python deconv_main.py

For the usage of baseline models or evaluation, please refer the corresponding folders (baseline and evaluation)

Please refer the notebook under the tutorial folder for running the codes of cell-type annotation task and deconvolution task, also the evaluation.

For the demo datasets, please use this link to download.

If you have questions, please contact Tianyu Liu or Zhiyuan Cao.

[email protected].

[email protected].