├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── Singularity ├── TODO.md ├── contributors.md ├── deploy.md ├── docs ├── _config.yml ├── assets │ ├── dyneusr_haxby_decoding.png │ ├── dyneusr_trefoil_knot.png │ ├── haxby_decoding_mapper_stages.png │ ├── logo.png │ ├── trefoil_knot_mapper_lens_0.png │ ├── trefoil_knot_mapper_lens_0_1.png │ ├── trefoil_knot_mapper_lens_0_2.png │ └── trefoil_knot_mapper_lens_1_2.png ├── demo │ ├── _config.yml │ ├── haxby-tsne │ │ ├── haxby_tsne.py │ │ └── index.html │ ├── haxby-umap-supervised │ │ ├── haxby_umap_supervised.py │ │ └── index.html │ ├── haxby-umap │ │ ├── haxby_umap.py │ │ └── index.html │ ├── index.md │ ├── trefoil-knot-custom-layouts │ │ ├── index.html │ │ └── trefoil_knot_custom_layouts.py │ └── trefoil-knot │ │ ├── index.html │ │ └── trefoil_knot.py └── index.md ├── dyneusr ├── __init__.py ├── _version.py ├── core.py ├── datasets │ ├── __init__.py │ └── trefoil.py ├── mapper │ ├── __init__.py │ ├── utils.py │ └── wrappers.py ├── tools │ ├── __init__.py │ ├── graph_utils.py │ ├── mixture.py │ └── networkx_utils.py └── visuals │ ├── __init__.py │ ├── annotation.py │ ├── plotting.py │ ├── templates │ ├── index-2D.html │ ├── index-3D.html │ ├── index-4D.html │ ├── index-save-svg.html │ └── index.html │ └── visualize.py ├── examples ├── force3D │ ├── custom_layouts.py │ ├── dyneusr2D_sphere.html │ ├── dyneusr3D_sphere.html │ ├── dyneusr4D_sphere.html │ ├── dyneusr_custom_layouts.html │ ├── dyneusr_sphere.html │ ├── sphere.py │ ├── sphere_2D.py │ ├── sphere_3D.py │ └── sphere_4D.py ├── haxby_decoding │ ├── custom_layouts.py │ ├── dyneusr4D_haxby_decoding.html │ ├── dyneusr_custom_layouts.html │ ├── dyneusr_haxby_decoding.html │ ├── dyneusr_haxby_decoding.png │ ├── haxby_decoding.py │ ├── haxby_decoding_4D.py │ └── mapper_stages.png ├── optimization │ └── optimizing-kmapper-with-dyneusr.ipynb └── trefoil_knot │ ├── compare_lenses.py │ ├── custom_layouts.py │ ├── dyneusr4D_trefoil_knot.html │ ├── 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