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.gitignore
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.DS_Store
.huskyrc.json
out
log.log
*.pkl
*.h5ad
*.gz
**/node_modules
*.pyc
*.vsix
envVars.txt
**/.vscode/.ropeproject/**
**/testFiles/**/.cache/**
*.noseids
.nyc_output
.vscode-test
__pycache__
npm-debug.log
**/.mypy_cache/**
!yarn.lock
coverage/
cucumber-report.json
**/.vscode-test/**
**/.vscode test/**
**/.vscode-smoke/**
**/.venv*/
port.txt
precommit.hook
pythonFiles/lib/**
pythonFiles/get-pip.py
debug_coverage*/**
languageServer/**
languageServer.*/**
bin/**
obj/**
.pytest_cache
tmp/**
.python-version
.vs/
test-results*.xml
xunit-test-results.xml
build/ci/performance/performance-results.json
!build/
debug*.log
debugpy*.log
pydevd*.log
nodeLanguageServer/**
nodeLanguageServer.*/**
dist/**
# translation files
*.xlf
package.nls.*.json
l10n/
# and repo specific
evaluation_experiments/EXP4_cibersort_eval.ipynb
evaluation_experiments/EXP4_bayesprism_eval.ipynb
functions/MCT_residual.R
preprocessing/EXP4_bayesprism_prep.ipynb
preprocessing/EXP4_cibersortprep.ipynb
results/EXP1/EXP1_eval_snadp_5CTnonoise.html
results/EXP1/EXP1_eval_snadp_5CTnonoise.ipynb
results/EXP2/EXP2_NNLS_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/EXP2_NNLS_pbmc_real.txt
results/EXP2/EXP2_bayesprism_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/EXP2_bayesprism_pbmc_real.txt
results/EXP2/EXP2_cibersort_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/EXP2_cibersortx_pbmc_real.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_real.txt
results/EXP2/selected_cells/EXP2_bayesprism_eval.ipynb
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_real.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_real.txt
esults/EXP2/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/EXP2_NNLS_pbmc_real.txt
results/EXP2/EXP2_bayesprism_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/EXP2_bayesprism_pbmc_real.txt
results/EXP2/EXP2_cibersort_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/EXP2_cibersortx_pbmc_real.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_real.txt
results/EXP2/selected_cells/EXP2_bayesprism_eval.ipynb
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_real.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_real.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_real.txt
results/EXP2/selected_cells/EXP2_bayesprism_eval.ipynb
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_real.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_real.txt
results/EXP1/EXP1_eval_snadp_5CTnonoise.html
results/EXP1/EXP1_eval_snadp_5CTnonoise.ipynb
results/EXP2/EXP2_NNLS_eval_pbmc_nonoise.ipynb
evaluation_experiments/EXP4_cibersort_eval.ipynb
evaluation_experiments/EXP4_bayesprism_eval.ipynb
functions/MCT_residual.R
preprocessing/EXP4_bayesprism_prep.ipynb
preprocessing/EXP4_cibersortprep.ipynb
results/EXP1/EXP1_eval_snadp_5CTnonoise.html
results/EXP1/EXP1_eval_snadp_5CTnonoise.ipynb
results/EXP2/EXP2_NNLS_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/EXP2_NNLS_pbmc_real.txt
results/EXP2/EXP2_bayesprism_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/EXP2_bayesprism_pbmc_real.txt
results/EXP2/EXP2_cibersort_eval_pbmc_nonoise.ipynb
results/EXP2/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/EXP2_cibersortx_pbmc_real.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_NNLS_pbmc_real.txt
results/EXP2/selected_cells/EXP2_bayesprism_eval.ipynb
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_bayesprism_pbmc_real.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_predicted.txt
results/EXP2/selected_cells/EXP2_cibersortx_pbmc_real.txt
data/EXP1/MCT_pbmc_EXP2_adata_scaden.txt
data/EXP1/cibersort/
data/EXP1/cibersort_results/
data/EXP1/pbmc3k/
data/EXP2/BP_results/
data/EXP2/BayesPrism/
data/EXP2/MCT_pbmc_EXP2_adata_scaden.txt
data/EXP2/SC3_v3_NextGem_SI_PBMC_10K_filtered_feature_bc_matrix.tar
data/EXP2/cibersort/
data/EXP2/cibersort_results/
data/EXP2/scaden/
data/EXP3/BP_results/
data/EXP3/BayesPrism/
data/EXP3/Hs.metadata.tsv
data/EXP3/MCT_adp_EXP3_2missing_realisticprop_noise_prop.csv
data/EXP3/MCT_adp_EXP3_2missing_realisticprop_noise_proprebal.csv
data/EXP3/cibersort/
data/EXP3/cibersort_results/
data/EXP4/CellMarker.csv
data/EXP4/MCT_hgsoc_EXP4_bulks.csv
data/EXP4/MCT_hgsoc_EXP4_dissociated_bulks.csv
data/EXP4/MCT_hgsoc_EXP4_dissociatedpolyA_bulks.csv
data/EXP4/MCT_hgsoc_EXP4_dissociatedpolya_bulks.csv
data/EXP4/MCT_hgsoc_EXP4_real_1missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_2missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_3missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_4missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_5missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_6missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_7missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_8missing_signal.txt
data/EXP4/MCT_hgsoc_EXP4_real_mixture.txt
data/EXP4/bulk/
data/EXP4/bulk_dissociated/
data/EXP4/bulk_dissociated_polyA/
data/EXP4/cibersort/
data/EXP4/cibersort_results/
data/EXP4/gene_maps.csv
data/EXP4/merged_bulks.csv
data/EXP4/merged_bulks_bygene.csv
data/EXP4/meta_bulks.csv
data/EXP4/single_cell/
environment/env_buddi.yml
evaluation_experiments/EXP2_scaden.sh
evaluation_experiments/EXP4_hgsoc_BayesPrism.R
evaluation_experiments/EXP5_eval.ipynb
evaluation_experiments/EXP5_eval_.ipynb
evaluation_experiments/error_SCADEN_EXP2.log
evaluation_experiments/output_SCADEN_EXP2.log
preprocessing/EXP5_HGSOC_fastq_processing/
preprocessing/figures/
results/EXP2EXP2_NNLS_pbmc_predicted.txt
results/EXP2EXP2_NNLS_pbmc_real.txt
results/EXP3/EXP3_NNLS_adp_random_noise_predicted.txt
results/EXP3/EXP3_NNLS_adp_random_noise_real.txt
results/EXP3/EXP3_NNLS_adp_random_nonoise_predicted.txt
results/EXP3/EXP3_NNLS_adp_random_nonoise_real.txt
results/EXP3/EXP3_NNLS_adp_realistic_noise_predicted.txt
results/EXP3/EXP3_NNLS_adp_realistic_noise_real.txt
results/EXP3/EXP3_NNLS_adp_realistic_nonoise_predicted.txt
results/EXP3/EXP3_NNLS_adp_realistic_nonoise_real.txt
results/EXP3/EXP3_bayesprism_adp_random_noise_predicted.txt
results/EXP3/EXP3_bayesprism_adp_random_noise_real.txt
results/EXP3/EXP3_bayesprism_adp_random_nonoise_predicted.txt
results/EXP3/EXP3_bayesprism_adp_random_nonoise_real.txt
results/EXP3/EXP3_bayesprism_adp_realistic_noise_predicted.txt
results/EXP3/EXP3_bayesprism_adp_realistic_noise_real.txt
results/EXP3/EXP3_bayesprism_adp_realistic_nonoise_predicted.txt
results/EXP3/EXP3_bayesprism_adp_realistic_nonoise_real.txt
results/EXP3/EXP3_cibersortx_adp_random_noise_predicted.txt
results/EXP3/EXP3_cibersortx_adp_random_noise_real.txt
results/EXP3/EXP3_cibersortx_adp_random_nonoise_predicted.txt
results/EXP3/EXP3_cibersortx_adp_random_nonoise_real.txt
results/EXP3/EXP3_cibersortx_adp_realistic_noise_predicted.txt
results/EXP3/EXP3_cibersortx_adp_realistic_noise_real.txt
results/EXP3/EXP3_cibersortx_adp_realistic_nonoise_predicted.txt
results/EXP3/EXP3_cibersortx_adp_realistic_nonoise_real.txt
results/EXP4/NMF_genes_residuals_bulks.xlsx
results/EXP5/