zcaiwei

Hi, I'm trying to apply NicheNet to my simulated dataset, but I'm getting the following error, can you tell me what the cause of the error is? The following is...

Hi, I ran into a bug at the last step. It seems it is caused by the loompy. But I followed the install instructions to install every package and the...

The plot of RNA velocity has no arrows

5

`Hi,` I'm having another problem when plotting RNA velocity. The following is my command: ``` cellDancer_df=cd.compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gene', expression_scale='power10', projection_neighbor_size=5, speed_up=(100,100)) fig, ax = plt.subplots(figsize=(10,10)) cdplt.scatter_cell(ax, cellDancer_df, colors=color_dict, alpha=0.5, s=30, velocity=True,...

The velocity1 and velocity2 values in celldancer_df are NaN

1

Hi, When I'm running the command `cellDancer_df=compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gene', expression_scale='power10', projection_neighbor_size=10, speed_up=(100,100))` , I'm having the following problem：  Can you tell me how to tune the parameter to avoid generating...

KeyError: 'Mu'

2

Hi, When I'm running `cdutil.adata_to_df_with_embed(adata, us_para=['Mu','Ms'], cell_type_para='celltype', embed_para='X_umap', save_path='cell_type_u_s.csv', gene_list=gene_list)` there is something wrong happened like " --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /tmp/ipykernel_3331/2728164412.py in 4 embed_para='X_umap', 5 save_path='cell_type_u_s.csv',...

ERROR Found in .addGeneScoreMat TmpGS for PBMC

2

**Describe the bug** Here's a bug I encountered creating ArrowFiles, the following is my code : ``` library(ArchR) addArchRGenome("hg38") if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") library(BSgenome.Hsapiens.UCSC.hg38) genomeAnnotation