├── .gitignore ├── CONTRIBUTIONS.md ├── Dockerfile ├── Fig1.jpg ├── LICENSE ├── Pipfile ├── Pipfile.lock ├── README.md ├── assets ├── dr.png ├── features.png ├── method.png ├── ti.png └── ud.png └── margaret ├── .gitignore ├── __init__.py ├── core.py ├── datasets ├── __init__.py ├── metric.py └── np.py ├── experiments ├── __init__.py ├── colon │ ├── files │ │ ├── go_absorptive_combined │ │ │ ├── GO_0.csv │ │ │ ├── GO_10.csv │ │ │ ├── GO_13.csv │ │ │ └── GO_8.csv │ │ ├── go_absorptive_ninflamed │ │ │ ├── GO_13.csv │ │ │ ├── GO_3.csv │ │ │ └── GO_5.csv │ │ ├── go_absorptive_normal │ │ │ ├── GO_1.csv │ │ │ ├── GO_10.csv │ │ │ ├── GO_13.csv │ │ │ ├── GO_3.csv │ │ │ ├── GO_8.csv │ │ │ └── GO_9.csv │ │ ├── go_goblet_inflammed │ │ │ ├── GO_0.csv │ │ │ ├── GO_1.csv │ │ │ ├── GO_2.csv │ │ │ └── GO_3.csv │ │ └── go_goblet_normal │ │ │ ├── GO_0.csv │ │ │ ├── GO_1.csv │ │ │ ├── GO_2.csv │ │ │ ├── GO_3.csv │ │ │ └── GO_4.csv │ ├── go_plot_absorptive_combined.py │ ├── go_plot_absorptive_ninflamed.py │ ├── go_plot_absorptive_normal.py │ └── go_plot_goblet.py ├── eb │ ├── __init__.py │ ├── bulk.py │ ├── files │ │ ├── bulk │ │ │ ├── TFs_AnimalTFDB.TXT │ │ │ ├── cd142pos.csv │ │ │ ├── cd49pos.csv │ │ │ ├── cd63pos.csv │ │ │ ├── cd82pos.csv │ │ │ ├── cd82pos_cd142pos.csv │ │ │ └── mapping.csv │ │ ├── go_26 │ │ │ ├── en_regex.txt │ │ │ ├── me_regex.txt │ │ │ └── nc_regex.txt │ │ └── go_5 │ │ │ ├── en_regex.txt │ │ │ ├── me_regex.txt │ │ │ └── nc_ne_regex.txt │ ├── go.py │ └── go_main.py └── topology │ ├── __init__.py │ ├── compare_global_topology.py │ ├── files │ ├── datasets_colab.csv │ └── datasets_kaggle.csv │ └── generate_plots.py ├── legacy ├── __init__.py ├── main.py └── models │ ├── ae.py │ ├── ae_variants.py │ ├── api.py │ ├── attention │ ├── __init__.py │ ├── multi_head_attention.py │ └── self_attention.py │ ├── diffmap.py │ └── layers.py ├── metrics ├── __init__.py ├── ipsen.py └── ordering.py ├── models ├── __init__.py ├── metric.py └── ti │ ├── __init__.py │ ├── connectivity.py │ ├── downstream.py │ ├── graph.py │ ├── pseudotime.py │ ├── pseudotime_v2.py │ └── sim.py ├── test.py ├── tests └── __init__.py ├── train_metric.py └── utils ├── R ├── generate_h5ad.r ├── generate_simulated.r └── monocle3.r ├── __init__.py ├── config.py ├── criterion.py ├── datastore.py ├── plot.py ├── trainer.py └── util.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zafar-Lab/Margaret/HEAD/.gitignore -------------------------------------------------------------------------------- /CONTRIBUTIONS.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Fig1.jpg: 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