.dockerignore
.gitattributes
.gitignore
.readthedocs.yaml
Dockerfile
LICENSE
MANIFEST.in
README.md
changelog.md
environment.yml
multiqc_config.yaml
package-lock.json
pyproject.toml
.github/workflows/conda.yaml
.github/workflows/docker.yaml
.github/workflows/release.yaml
.vscode/launch.json
.vscode/settings.json
conda/recipe/bld.bat
conda/recipe/build.sh
conda/recipe/conda_build_config.yaml
conda/recipe/meta.yaml
configs/config.yaml
docs/build/Makefile
docs/build/_templates
docs/build/about.rst
docs/build/changelog.rst
docs/build/conf.py
docs/build/gui.rst
docs/build/implement_new_models.rst
docs/build/imputer_methods.rst
docs/build/index.rst
docs/build/install.rst
docs/build/make.bat
docs/build/modules.rst
docs/build/non_ml_imputers.rst
docs/build/pgsui.data_processing.rst
docs/build/pgsui.impute.rst
docs/build/pgsui.impute.supervised.imputers.rst
docs/build/pgsui.impute.supervised.rst
docs/build/pgsui.impute.unsupervised.imputers.rst
docs/build/pgsui.impute.unsupervised.models.rst
docs/build/pgsui.impute.unsupervised.rst
docs/build/pgsui.rst
docs/build/pgsui.utils.rst
docs/build/supervised_imputers.rst
docs/build/tutorial.rst
docs/build/unsupervised_imputers.rst
docs/build/_static/custom.css
img/NLPCA_Model_Architecture.svg
img/VAE_Model_Architecture_rotated.svg
img/pgsui-logo-faded-thumb.png
img/pgsui-logo-faded.png
img/pgsui-logo-notfaded.png
notebooks/run_pgsui_dev.ipynb
pg_sui.egg-info/PKG-INFO
pg_sui.egg-info/SOURCES.txt
pg_sui.egg-info/dependency_links.txt
pg_sui.egg-info/entry_points.txt
pg_sui.egg-info/requires.txt
pg_sui.egg-info/top_level.txt
pgsui/__init__.py
pgsui/_version.py
pgsui/cli.py
pgsui/data_processing/__init__.py
pgsui/data_processing/config.py
pgsui/data_processing/containers.py
pgsui/data_processing/transformers.py
pgsui/electron/bootstrap.py
pgsui/electron/launch.py
pgsui/electron/package.json
pgsui/electron/app/__init__.py
pgsui/electron/app/__main__.py
pgsui/electron/app/main.js
pgsui/electron/app/package-lock.json
pgsui/electron/app/package.json
pgsui/electron/app/preload.js
pgsui/electron/app/server.py
pgsui/electron/app/extra-resources/.gitkeep
pgsui/electron/app/icons/icons/1024x1024.png
pgsui/electron/app/icons/icons/128x128.png
pgsui/electron/app/icons/icons/16x16.png
pgsui/electron/app/icons/icons/24x24.png
pgsui/electron/app/icons/icons/256x256.png
pgsui/electron/app/icons/icons/32x32.png
pgsui/electron/app/icons/icons/48x48.png
pgsui/electron/app/icons/icons/512x512.png
pgsui/electron/app/icons/icons/64x64.png
pgsui/electron/app/icons/icons/icon.icns
pgsui/electron/app/icons/icons/icon.ico
pgsui/electron/app/ui/logo.png
pgsui/electron/app/ui/renderer.js
pgsui/electron/app/ui/styles.css
pgsui/electron/app/ui/ui_shim.js
pgsui/example_data/__init__.py
pgsui/example_data/phylip_files/__init__.py
pgsui/example_data/phylip_files/test.phy
pgsui/example_data/popmaps/__init__.py
pgsui/example_data/popmaps/phylogen_nomx.popmap
pgsui/example_data/structure_files/__init__.py
pgsui/example_data/structure_files/test.pops.2row.allsites.str
pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz
pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi
pgsui/impute/__init__.py
pgsui/impute/deterministic/imputers/allele_freq.py
pgsui/impute/deterministic/imputers/mode.py
pgsui/impute/deterministic/imputers/nmf.py
pgsui/impute/deterministic/imputers/phylo.py
pgsui/impute/deterministic/imputers/ref_allele.py
pgsui/impute/supervised/__init__.py
pgsui/impute/supervised/base.py
pgsui/impute/supervised/imputers/__init__.py
pgsui/impute/supervised/imputers/hist_gradient_boosting.py
pgsui/impute/supervised/imputers/random_forest.py
pgsui/impute/unsupervised/__init__.py
pgsui/impute/unsupervised/base.py
pgsui/impute/unsupervised/callbacks.py
pgsui/impute/unsupervised/loss_functions.py
pgsui/impute/unsupervised/nn_scorers.py
pgsui/impute/unsupervised/imputers/__init__.py
pgsui/impute/unsupervised/imputers/autoencoder.py
pgsui/impute/unsupervised/imputers/nlpca.py
pgsui/impute/unsupervised/imputers/ubp.py
pgsui/impute/unsupervised/imputers/vae.py
pgsui/impute/unsupervised/models/__init__.py
pgsui/impute/unsupervised/models/autoencoder_model.py
pgsui/impute/unsupervised/models/nlpca_model.py
pgsui/impute/unsupervised/models/ubp_model.py
pgsui/impute/unsupervised/models/vae_model.py
pgsui/utils/__init__.py
pgsui/utils/classification_viz.py
pgsui/utils/logging_utils.py
pgsui/utils/misc.py
pgsui/utils/plotting.py
pgsui/utils/pretty_metrics.py
pgsui/utils/scorers.py
scripts/build_gui_dists.zsh
scripts/download_training_data.zsh
scripts/pg_sui.py
scripts/run_iqtree.zsh
scripts/start_pgsui.sh
scripts/stop_pgsui.sh
scripts/summarize_input_metadata.py
scripts/vcf2phy.py
scripts/vcf2phy.zsh
snpiosp/__init__.py
snpiosp/compare_dataset_stats.py
snpiosp/run_snpiosp.py
snpiosp/snpiosp.py
tests/conftest.py
tests/test_config.py
tests/test_deterministic_imputers.py
tests/test_imputers_unsupervised.py
tests/test_scorers.py
tests/test_transformers.py
workflow/run_sim1.smk
workflow/sim1_config.yaml
workflow/t0.01_c0.1_a0.0_gtrgamma.phylip
workflow/envs/tree_sim.yml
workflow/profile/config.yaml
workflow/scripts/sim_treeparams.py