├── Benchmarks ├── .DS_Store ├── Complexity │ ├── Complexity_benchmark.Rmd │ ├── Complexity_stats.Rmd │ ├── Objects_generation.ipynb │ ├── SaveR2G.ipynb │ ├── UMAPs.ipynb │ ├── WriteDARs.ipynb │ ├── pycisTopic_benchmark.ipynb │ ├── pycistarget_benchmark.ipynb │ └── scenicplus_benchmark.ipynb ├── DEM │ ├── Show_case_DEM.ipynb │ └── illuminati.Rmd ├── Hi-C_analysis │ └── HiC_processing.ipynb ├── Perturbation_analysis.Rmd ├── SCENIC+ │ ├── 0.1_export_cellTopic.ipynb │ ├── 0.2_format data.Rmd │ ├── 0.UMAP.Rmd │ ├── 1.TF_recovery.Rmd │ ├── 1.TF_recovery_v2.Rmd │ ├── 1.pycisTopic.ipynb │ ├── 1_FigR_Encode_lines.Rmd │ ├── 1_FigR_Encode_lines_2.Rmd │ ├── 2.Region_to_gene.Rmd │ ├── 2.pycisTarget_V10-V2.ipynb │ ├── 3.SCENIC+-V10-V2.ipynb │ ├── 3.TF-to-region_V2.Rmd │ ├── 4.TF_perturb.Rmd │ ├── CellOracle.md │ ├── DESEQ.Rmd │ ├── Dotplot_eGRN.Rmd │ ├── Form_regulons.Rmd │ ├── Gene_expression_prediction.ipynb │ ├── Granie.Rmd │ ├── Methods_benchmark.Rmd │ ├── Pando.md │ ├── Perturbation_simulations.ipynb │ ├── SCENIC+_TF_network.ipynb │ ├── TracksVSMotif_benchmark.Rmd │ └── count_perturbation_datasets.Rmd ├── cisTarget_benchmark │ ├── Motif_benchmark.ipynb │ └── Public_motif_benchmark.ipynb └── cisTopicVSpycisTopic │ ├── .DS_Store │ └── cisTopicVSpycisTopic_speedtest.Rmd ├── EAD ├── Differentiation_tutorial-v2-streamplot.ipynb ├── MultiVelo.ipynb ├── MultiVelo_python.ipynb └── SCENIC+_TF_network.ipynb ├── Figure_2.md ├── Figure_4.md ├── Figure_5.md ├── Human_cerebellum ├── .DS_Store ├── 1.RNA-VSN.ipynb ├── 2.pycisTopic.ipynb ├── 3.pycistarget_scenic+_human_brain_seurat.ipynb ├── VSN │ ├── FixLoom.Rmd │ ├── FixLoom.nb.html │ ├── single_sample_scenic.config │ ├── single_sample_scenic_filtered_loom.config │ └── single_sample_scrublet.config └── networks2cytoscape.ipynb ├── Motif_collection ├── Suppl_plots.Rmd └── motif_clustering_20121.Rmd ├── MouseVSHumanBrain ├── 1.Cortex_pycisTopic.ipynb ├── 2.Cortex_cistarget+SCENIC+.ipynb ├── Cell_pairing.ipynb ├── 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