.dockerignore
.gitignore
LICENSE
MANIFEST.in
README.md
setup.py
benchmarking/harmonization.ipynb
benchmarking/metrics.ipynb
benchmarking/model_evaluation.ipynb
benchmarking/tool_running.ipynb
benchmarking/tools/run_seurat_workflow.R
deployment/deploy.sh
dinglab-pollock/meta.yaml
dinglab-pollock/post-link.bat
dinglab-pollock/post-link.sh
dinglab_pollock.egg-info/PKG-INFO
dinglab_pollock.egg-info/SOURCES.txt
dinglab_pollock.egg-info/dependency_links.txt
dinglab_pollock.egg-info/entry_points.txt
dinglab_pollock.egg-info/top_level.txt
docker/cpu/Dockerfile
docker/cpu/Dockerfile_v2
docker/cpu/bvae
docker/gpu/Dockerfile
docker/gpu/bvae
docker/gpu/vae_dockerfile
examples/pbmc_model_training.ipynb
examples/pbmc_module_prediction.ipynb
examples/pollock_module_examination.ipynb
examples/pollock_module_explain.ipynb
examples/rpollock_pbmc_prediction.Rmd
examples/.ipynb_checkpoints/pbmc_model_training-checkpoint.ipynb
examples/.ipynb_checkpoints/pbmc_module_prediction-checkpoint.ipynb
examples/.ipynb_checkpoints/pollock_module_examination-checkpoint.ipynb
images/polluck.png
notebooks/Untitled.ipynb
notebooks/Untitled1.ipynb
notebooks/atacseq_integration.ipynb
notebooks/basic usage - pretrained model.ipynb
notebooks/breast_stemness_bvae-v2.ipynb
notebooks/breast_stemness_bvae-v3.ipynb
notebooks/breast_stemness_bvae.ipynb
notebooks/bvae.ipynb
notebooks/ccrcc_stemness.ipynb
notebooks/cell_type_accuracy.ipynb
notebooks/cross_dataset_model_comparison.ipynb
notebooks/cytotrace check.ipynb
notebooks/data cleaning.ipynb
notebooks/dataset_processing.ipynb
notebooks/example_from_expression_table.ipynb
notebooks/h5ad_staging.ipynb
notebooks/model_integration.ipynb
notebooks/module_combining.ipynb
notebooks/module_training.ipynb
notebooks/nugyen parsing.ipynb
notebooks/pancreas_example.ipynb
notebooks/pbmc_example.ipynb
notebooks/pbmc_model_training-Copy1.ipynb
notebooks/pbmc_module_prediction-Copy1.ipynb
notebooks/pollock module testing.ipynb
notebooks/pollock_atacseq.ipynb
notebooks/pollock_module_prediction.ipynb
notebooks/sandbox.ipynb
notebooks/scgen_vae_pollock_testing.ipynb
notebooks/sn_sc_integration.ipynb
notebooks/stemness.ipynb
notebooks/test_notebook.Rmd
notebooks/test_notebook.nb.html
notebooks/vae_pollock_test.ipynb
pollock/__init__.py
pollock/pollock.R
pollock/pollock.py
pollock/pollock_setup.py
pollock/models/__init__.py
pollock/models/analysis.py
pollock/models/explain.py
pollock/models/model.py
pollock/preprocessing/__init__.py
pollock/preprocessing/preprocessing.py
pollock/wrappers/__init__.py
pollock/wrappers/encoder_shaps.py
pollock/wrappers/explain_rds.R
pollock/wrappers/predict_rds.R
pollock/wrappers/rwrappers.py
pollock/wrappers/train_rds.R
tests/test_pollock.py
tests/data/dummy.h5ad
tests/data/dummy.rds
tests/data/dummy_small.h5ad
tests/data/dummy_small.rds