├── .gitattributes ├── .gitignore ├── LICENSE.md ├── README.md ├── docs ├── README.md ├── assets │ └── Figure_8_Revised.png ├── envs │ └── tutorial.yaml ├── guidelines.Rmd ├── guidelines.html └── guidelines.pdf └── workflow ├── Snakefile ├── analysis ├── R │ ├── 05_Iniq_Control_Fig_2_Analysis_Plots.R │ ├── 06_Iniq_Control_Fig_2_Analysis_Stat_Tests.R │ ├── 07_Iniq_Control_Fig_3_Analysis_Plots.R │ ├── 08_Iniq_Control_Fig_3_Analysis_Stat_Tests.R │ ├── 09_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R │ ├── 10B_Iniq_Real_Datasets_Fig_4_Stat_Tests.R │ ├── 10_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R │ ├── 12B_Iniq_PDAC_Fig_6_Stat_Tests.R │ ├── 12_Fig_6_PDAC_Analysis_Plots.R │ ├── 13_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R │ ├── 19_Supplementary_TI_Analysis.R │ ├── 20_Fig_6_PDAC_Reanno_Analysis_Plots.R │ ├── 21_Fig_6_PDAC_Reanno_Stats_Tests.R │ ├── 21_PBMC_perturbation_umap_plots.R │ └── knn_example.R └── python │ └── 01_Fig_7_Imbal_Metric_Analysis.ipynb ├── configs ├── config.json ├── config_control.json ├── config_control_ti_only.json ├── config_custom.json ├── config_lowcap.json ├── config_lowcap_control_like.json ├── config_lowcap_modified.json ├── config_lowcap_modified_pdac_reanno.json ├── config_pdac_comp.json ├── config_pdac_comp_reanno.json ├── config_umap.json ├── test_config.json └── test_config_lite.json ├── envs ├── analysis.yaml └── integrate.yaml ├── preprocessing └── pdac │ ├── Snakefile │ └── preprocess_env.yaml ├── scripts └── python │ ├── annotation_results.py │ ├── annotation_scoring.py │ ├── celltype_imbalance_summary.py │ ├── clustering_concordance.py │ ├── clustering_stats.py │ ├── dge_concordance_full.py │ ├── dge_concordance_stats.py │ ├── dge_ranking_concordance.py │ ├── dge_ranking_marker_subset.py │ ├── dge_ranking_per_cluster.py │ ├── downsample_summary.py │ ├── imbalance_summary.py │ ├── integrate_data.py │ ├── integrate_data_paga.py │ ├── knn_classification.py │ ├── marker_get.py │ ├── reference_annotation.py │ ├── reference_control_annotation.py │ ├── relatedness_metric.py │ ├── ti_concordance.py │ └── umap_plots.py └── src ├── R ├── liger_integrate.R ├── seurat_integrate.R └── seurat_reference_map.R └── python ├── __init__.py ├── imbalanced_clustering ├── __init__.py ├── ami.py ├── ari.py ├── utils │ ├── __init__.py │ ├── _emi_cython.pyx │ ├── avg.py │ ├── checks.py │ ├── contingency.py │ └── mi.py └── vmeasure.py ├── loaders └── rna_data.py └── utils ├── __init__.py ├── cluster_concordance.py ├── clustering.py ├── diffexp.py ├── integrate.py ├── integrate_ti.py ├── kmeans.py ├── liger_integrate.py ├── mnn.py ├── relatedness.py ├── sample.py ├── seurat_integrate.py ├── seurat_reference_mapping.py └── umap.py /.gitattributes: -------------------------------------------------------------------------------- 1 | workflow/analysis/** linguist-vendored 2 | -------------------------------------------------------------------------------- /.gitignore: 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