DIALOGUE
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livnatje
DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
Hello, First of all, thanks for the great tool and thank you for your research! I’d like to know whether this tool has a limit on the number of single...
Hello, The selection of sparse canonical variates in the Methods section of your paper details that $w_i$ and $w_j$ are fit according to the multi-factor PMD algorithm in Witten 2009....
The analysis runs fine, but when finilizing the analysis I run into trouble: "#************Finalizing the scores************#" [1] "Removing MCP2" [1] "Removing MCP3" [1] "Removing MCP4" [1] "Removing MCP5" [1] "Removing...
Hi @livnatje, We are trying to reproduce the Nanostring SMI results in the Nature Biotechnology paper but seems that our results are quite different compared to what was reported in...
Dear Dr livnatje: Thank you for your wonderful software, when I run the DIALOGUE.run,the error report: ... [1] "#************DIALOGUE Step II (multilevel modeling): Hepatocyte vs. Stellate ************#" [1] "1 MCPs...
If any of the MCPs are present in just a subset of cell types, pairs.plot returns an error. I added a line to DIALOGUE.plot.av that removes any columns that are...
The new version is not user-friendly, the old version was better.
Dear DIALOGUE team, i want to run make.cell.type with tpm being a sparse matrix (dgRMatrix or dgCMatrix). When running with the loaded make.cell.type method I get the following error (when...
Hey, X needs to have colnames for this line https://github.com/livnatje/DIALOGUE/blob/9c146ccf28d7706aaa60d00947a9126b4e75fd69/R/DIALOGUE.main.R#L155 which was not obvious to me and took quite some time to figure out. Could you maybe assign it random...
Is it possible to provide the code for the putative cell–cell interactions mediated by ligand–receptor binding? We would really like to try out Dialogue for cell-cell communication. All the best,...
