mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.
Revue : Bioinformatics (Oxford, England)
Parution : Samedi 1 août 2026
Statut : code vérifié
Méthodes : Statistiques, Lissage, filtrage d'état, décompositions, Apprentissage
Carte de traçage
Proposée automatiquement : ces liens ont été trouvés dans l'article et vérifiés à la source, sans relecture humaine. Elle recevra un DOI Zenodo quand un de ses auteurs l'aura validée avec son ORCID.
Code des auteurs
nomuhyooon/mmvelo
Licence : aucune : les auteurs gardent tous leurs droits
État : le lien répond
Preuve : fichiers inventoriés
Commit :
3dbe5d18cad3e2f020df8e8b74f3068f669b3b7fLangages : Python (81), Jupyter (3)
Trouvé : « Data availability »
85 fichiers, à lire à la source
Ce dépôt n'a pas de licence : ses auteurs gardent tous leurs droits. Lisez-le à la source.
- mmVelo_tutorial/src/dataset.py — Python, 226 lignes
- mmVelo_tutorial/src/funcs.py — Python, 115 lignes
- mmVelo_tutorial/src/models.py — Python, 556 lignes
- mmVelo_tutorial/src/modules.py — Python, 201 lignes
- mmVelo_tutorial/src/streamlineplot.py — Python, 1 722 lignes
- mmVelo_tutorial/src/train.py — Python, 265 lignes
- mmVelo_tutorial/src/utils.py — Python, 938 lignes
- mmVelo_tutorial/tutorial.ipynb — Jupyter, 110 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/000_performance_evaluation.py — Python, 252 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/00_get_inferred_data.py — Python, 237 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/01_clustering.py — Python, 122 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/02_pseudotime.py — Python, 236 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/03_peak_gene_linkage.py — Python, 50 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/04_plot_expr_umap.py — Python, 274 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/04_plot_expr_umap_for_fig.py — Python, 391 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/05_peak_annotation.py — Python, 175 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag.py — Python, 365 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering.py — Python, 242 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering_preliminary.py — Python, 201 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering_sep_concat.py — Python, 294 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_confidence.py — Python, 177 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_ipc.py — Python, 366 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_leiden.py — Python, 594 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_naive_heatmap.py — Python, 755 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/07_leiden_promoter.py — Python, 206 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/07_motif_velocity.py — Python, 445 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/08_benchmarking_latent.py — Python, 440 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/09_dadt_clustering_heatmap.py — Python, 361 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/09_dadt_clustering_heatmap_for_fig.py — Python, 368 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/10_streamline_plot.py — Python, 92 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/11_neurod2_modality.py — Python, 528 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/12_dadt_clustering_for_great.py — Python, 42 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/20_mmvelo_ablation_analysis.py — Python, 673 lignes
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/21_clusterwise_mean_velocity.py — Python, 214 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/000_performance_evaluation.py — Python, 385 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/00_get_inferred_adata.py — Python, 299 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/01_clustering_pseudotime.py — Python, 202 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/02_missingmodality_streamline.py — Python, 200 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/03_heatmap.py — Python, 520 lignes
- mmVelo_tutorial_v2/src/fig_human_brain/04_inter_patient_analysis.py — Python, 224 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/000_performace_evaluation.py — Python, 356 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/00_get_inferred_data.py — Python, 346 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/01_annotate_peudotime.py — Python, 96 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/01_subclusterring_tacs.py — Python, 103 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/02_clustering_heatmap.py — Python, 699 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif.py — Python, 622 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif_chromvar.py — Python, 381 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif_vjp.py — Python, 574 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/04_clustering_motif_svd.py — Python, 95 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference.py — Python, 508 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_1st.py — Python, 399 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_count.py — Python, 517 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_pycistopic_res.py — Python, 601 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_sep.py — Python, 592 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_Lef1.py — Python, 74 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_crate_filtered_bed.py — Python, 88 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_filter_peaks_for_plot.py — Python, 72 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_off_manifold.py — Python, 231 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_off_manifold_mod.py — Python, 250 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_uncertainty.py — Python, 236 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/07_uncertainty_vs_pseudotime.py — Python, 249 lignes
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/20_mmvelo_ablation_analysis.py — Python, 681 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_multi/funcs.py — Python, 115 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/models.py — Python, 574 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/modules.py — Python, 201 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/streamlineplot.py — Python, 1 724 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/utils.py — Python, 939 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_off_manifold.py — Python, 339 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_off_manifold_mod.py — Python, 490 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_uncertainty.py — Python, 476 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/dataset_all_modality.py — Python, 364 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/models_missingmodality_all_adv_modadv.py — Python, 611 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/modules.py — Python, 248 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/streamlineplot.py — Python, 1 724 lignes
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/utils.py — Python, 792 lignes
- mmVelo_tutorial_v2/src/mmvelo_tutorial/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_tutorial/dataset_mouse_brain.py — Python, 164 lignes
- mmVelo_tutorial_v2/src/mmvelo_tutorial/train_human_brain.py — Python, 468 lignes
- mmVelo_tutorial_v2/src/mmvelo_tutorial/train_mouse_brain.py — Python, 349 lignes
- mmVelo_tutorial_v2/src/mmvelo_tutorial/viz_human_brain.py — Python, 267 lignes
- mmVelo_tutorial_v2/tutorial_1_mouse_brain.ipynb — Jupyter, 350 lignes
- mmVelo_tutorial_v2/tutorial_2_human_brain_missing_modality.ipynb — Jupyter, 396 lignes
- README.md — Texte, 319 lignes
Zenodo 20103609
Licence : CC-BY-4.0
État : le lien répond
Preuve : fichiers inventoriés
Trouvé : « Data availability »
85 fichiers
- mmVelo_tutorial/src/dataset.py — Python, 226 lignes [lire ici]
- mmVelo_tutorial/src/funcs.py — Python, 115 lignes [lire ici]
- mmVelo_tutorial/src/models.py — Python, 556 lignes [lire ici]
- mmVelo_tutorial/src/modules.py — Python, 201 lignes [lire ici]
- mmVelo_tutorial/src/streamlineplot.py — Python, 1 722 lignes [lire ici]
- mmVelo_tutorial/src/train.py — Python, 265 lignes [lire ici]
- mmVelo_tutorial/src/utils.py — Python, 938 lignes [lire ici]
- mmVelo_tutorial/tutorial.ipynb — Jupyter, 110 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/000_performance_evaluation.py — Python, 252 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/00_get_inferred_data.py — Python, 237 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/01_clustering.py — Python, 122 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/02_pseudotime.py — Python, 236 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/03_peak_gene_linkage.py — Python, 50 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/04_plot_expr_umap.py — Python, 274 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/04_plot_expr_umap_for_fig.py — Python, 391 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/05_peak_annotation.py — Python, 175 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag.py — Python, 365 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering.py — Python, 242 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering_preliminary.py — Python, 201 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_clustering_sep_concat.py — Python, 294 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_confidence.py — Python, 177 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_ipc.py — Python, 366 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_leiden.py — Python, 594 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/06_time_lag_naive_heatmap.py — Python, 755 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/07_leiden_promoter.py — Python, 206 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/07_motif_velocity.py — Python, 445 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/08_benchmarking_latent.py — Python, 440 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/09_dadt_clustering_heatmap.py — Python, 361 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/09_dadt_clustering_heatmap_for_fig.py — Python, 368 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/10_streamline_plot.py — Python, 92 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/11_neurod2_modality.py — Python, 528 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/12_dadt_clustering_for_great.py — Python, 42 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/20_mmvelo_ablation_analysis.py — Python, 673 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_E18_mose_brain/21_clusterwise_mean_velocity.py — Python, 214 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/000_performance_evaluation.py — Python, 385 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/00_get_inferred_adata.py — Python, 299 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/01_clustering_pseudotime.py — Python, 202 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/02_missingmodality_streamline.py — Python, 200 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/03_heatmap.py — Python, 520 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_human_brain/04_inter_patient_analysis.py — Python, 224 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/000_performace_evaluation.py — Python, 356 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/00_get_inferred_data.py — Python, 346 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/01_annotate_peudotime.py — Python, 96 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/01_subclusterring_tacs.py — Python, 103 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/02_clustering_heatmap.py — Python, 699 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif.py — Python, 622 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif_chromvar.py — Python, 381 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/03_clustering_motif_vjp.py — Python, 574 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/04_clustering_motif_svd.py — Python, 95 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference.py — Python, 508 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_1st.py — Python, 399 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_count.py — Python, 517 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_pycistopic_res.py — Python, 601 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_GRN_inference_sep.py — Python, 592 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_Lef1.py — Python, 74 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_crate_filtered_bed.py — Python, 88 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/05_post_GRN_filter_peaks_for_plot.py — Python, 72 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_off_manifold.py — Python, 231 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_off_manifold_mod.py — Python, 250 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/06_velocity_uncertainty.py — Python, 236 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/07_uncertainty_vs_pseudotime.py — Python, 249 lignes [lire ici]
- mmVelo_tutorial_v2/src/fig_mouse_hair_follicle/20_mmvelo_ablation_analysis.py — Python, 681 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_multi/funcs.py — Python, 115 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/models.py — Python, 574 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/modules.py — Python, 201 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/streamlineplot.py — Python, 1 724 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/utils.py — Python, 939 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_off_manifold.py — Python, 339 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_off_manifold_mod.py — Python, 490 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi/velocity_uncertainty.py — Python, 476 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/dataset_all_modality.py — Python, 364 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/models_missingmodality_all_adv_modadv.py — Python, 611 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/modules.py — Python, 248 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/streamlineplot.py — Python, 1 724 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_multi_cond/utils.py — Python, 792 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_tutorial/__init__.py — Python, 1 ligne
- mmVelo_tutorial_v2/src/mmvelo_tutorial/dataset_mouse_brain.py — Python, 164 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_tutorial/train_human_brain.py — Python, 468 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_tutorial/train_mouse_brain.py — Python, 349 lignes [lire ici]
- mmVelo_tutorial_v2/src/mmvelo_tutorial/viz_human_brain.py — Python, 267 lignes [lire ici]
- mmVelo_tutorial_v2/tutorial_1_mouse_brain.ipynb — Jupyter, 350 lignes [lire ici]
- mmVelo_tutorial_v2/tutorial_2_human_brain_missing_modality.ipynb — Jupyter, 396 lignes [lire ici]
- README.md — Texte, 318 lignes [lire ici]