dynamo-release
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aristoteleo
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
Hello dynamo. I met this issue when trying to run the scNT-seq human hematopoiesis. What should I do to change the dtype from object to float? Thank you very much....
Hello Dynamo, I can get `pearson_transition_matrix` by running `dyn.tl.cell_velocities(adata, basis='umap', n_neighbors = 10, method='pearson', other_kernels_dict={'transform': 'sqrt'})`. Your amazing tutorial has already shown the way to compute vector field pseudotime based...
Hello dynamo， I ran into this problem when trying to run our dataset. What do you suggest? thank you very much. My code process is as follows, import warnings warnings.filterwarnings('ignore')...
Hello Dynamo, In the LAP tutorial, the example datasets has `adata.obsp['X_umap_distances']` and `adata.obsp['cosine_transition_matrix']`. ```python adata = dyn.sample_data.hematopoiesis() adata obsp: 'X_umap_connectivities', 'X_umap_distances', 'connectivities', 'cosine_transition_matrix', 'distances', 'fp_transition_rate', 'moments_con', 'pca_ddhodge', 'perturbation_transition_matrix', 'umap_ddhodge' ```...
Hello! I am following the LAP tutorial, and keep running into an issue with `dyn.pd.least_action`. Please let me know if I should provide more information, and I hope there is...
Hi Xiaojie, Could you show me how to set the "cell" parameter so I can do In silico perturbation in selected cell populations (for example, cluster1)? Thanks!
Dear authors, I tried `'full reg'/ 'full eff'` modes in the `dyn.vf.rank_jacobian_genes()` function ``` full_reg_rank = dyn.vf.rank_jacobian_genes(abm2, groups='ann0608', mode="full reg", abs=False, output_values=True, return_df=True) full_eff_rank = dyn.vf.rank_jacobian_genes(abm2, groups='ann0608', mode='full eff', abs=False,...
**Recruiting Python Programmers to Develop Predictive Single Cell Spatiotemporal Analysis Toolkit** The Weissman lab (https://weissman.wi.mit.edu/) at Whitehead Institute & MIT is looking for one or more talented programmer (primarily undergraduates/masters...
The dynamo is working perfectly on my Intel Mac but on M1 (ARM based) mac, upon calling `dyn.tl.dynamics(adata)`, it throws the following error: `OMP: Info #271: omp_set_nested routine deprecated, please...
Hello Dynamo, I understand that a vector field is a continuous function that describes the cell fate in PCA or UMAP space. But how shall we interpret the vectors going...
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Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses