cell2cell
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earmingol
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Hi Erick, The choice of upper_rank has a significant impact on the automatically determined rank. They go in the same direction. How would one make the choice of upper_rank in...
Hi Erick, In your example https://github.com/earmingol/cell2cell/blob/master/examples/tensor_cell2cell/Tensor-cell2cell-PBMC.ipynb, it is suggested to "sort contexts to have them all together by condition, but donors in the same order within each condition". How important...
Hi cell2cell team, Fantastic work on the package - it is really addressing a missing gap in current cell-cell interaction tools! I had an issue with running tensorcell2cell and was...
Hello, I'm running tensor-cell2cell with liana and have done successfully for one of my datasets. For a second dataset, I have 7 cell types but only the same 3 are...
Hello, I encoutered a warning today with this code interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq.to_df().T, ppi_data=lr_pairs, metadata=meta, interaction_columns=('ligand_symbol', 'receptor_symbol'), communication_score='expression_thresholding', expression_threshold=0.1, # values after aggregation cci_score='bray_curtis', cci_type='undirected', aggregation_method='nn_cell_fraction', barcode_col='index', celltype_col='celltype', complex_sep='&', verbose=False) And...
Tensor output of `c2c.analysis.run_tensor_cell2cell_pipeline` works fine but loading it from the .pkl file doesn't Can reproduce this error in the package's colab demo.
Hello, I am not sure whether I should post this error here or on the Basilisk Github page, so please feel free to let me know. I am running the...
The memory at each iteration seems to accumulate. Is it possible to release it or chuck it differently to circumvent this issue? ``` Running Elbow Analysis 24%|██▍ | 6/25 [23:50...
hello, I'm using cell2cell to identify interactions with scRNAseq data. ``` interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq, ppi_data=lr_pairs, metadata=meta, interaction_columns=( 'source_genesymbol', 'target_genesymbol'), communication_score='expression_gmean', cci_score='bray_curtis', cci_type='directed', aggregation_method='average', barcode_col='index', celltype_col=args.annot, complex_sep='_', verbose=True) ``` When I...
Hello, I would like to know if it's possible to do some interaction heatmap plot and PCoA Euclidean space plot with the new tutorial on ASD with Factor map. I...
