Yuanjian Huang
Yuanjian Huang
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, 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 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...
Hello Dynamo, I was running the `Cell-wise analyses` tutorial. It was smooth until the Response heatmap. I got a `TypeError: Image data of dtype object cannot be converted to float`....
Hello Dynamo, When setting the initial cells and target cells for LAP, the fixed points which represent the cell state should be defined. I chose the fixed points 13, 6,...
Hello Dynamo, I'm wondering whether we have a detailed tutorial for plotting lineage tree of hematopoiesis (https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_megakaryocytes_appearance/tutorial_hsc_dynamo_megakaryocytes_appearance.html). Thanks! Best, YJ I did like this. ```python dyn.pd.tree_model(adata, group='cell_type', progenitor='HSC', terminators=["Meg", "Ery",...
Hello Dynamo, When I was running this tutorial (https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_basophil_lineage/tutorial_hsc_dynamo_basophil_lineage.html), only 4 rows of switch gene-pairs were found. There is no GATA2-PLEK pair like the tutorial said. Do I miss something?...
Hello pyscenic, For the heatmap (coding below), is it possible to sort it by cell type colors? I mean the cells from the same cell types aggregate together to make...
Hello @sunduanchen We performed several rounds of Scissor analysis, but we still don't know what is the best rule for determining the best percentage of Scissor selected cells? For example,...
Hello RGT, Thanks for developing this amazing package. I met the error `KeyError: "sequence 'chr22' not present"` when following the full-site test tutorial here (http://www.regulatory-genomics.org/motif-analysis/introduction/). Could you please help me...