multinichenetr
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saeyslab
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Hi, Thanks again for the great package. I have a quick question on how to manually adjust the range (or the scale) of what I plot (eg. scaled ligand activity,...
Parellelization seems stalled @maartenciers in case you encounter this issue: run the function with one core only in serial way
Hi, First of all, thank you for developing this package. Hope you can help me with the following: when calling multi_nichenet_analysis() my process keeps getting killed due to memory problems....
Hello, I am trying to run the DE analysis with 3 conditions. One conditions has a condition-specific cell type (adipocyte). In the corresponding vignette for condition-specific cell types, you mention...
``` contrasts_oi = c("'P-(A+B+C+D+T)/5','A-(P+B+C+D+T)/5','B-(A+P+C+D+T)/5','C-(A+B+P+D+T)/5','D-(A+B+C+P+T)/5','T-(A+B+C+D+P)/5'") contrast_tbl = tibble(contrast = c("P-(A+B+C+D+T)/5","A-(P+B+C+D+T)/5", "B-(A+P+C+D+T)/5","C-(A+B+P+D+T)/5","D-(A+B+C+P+T)/5","T-(A+B+C+D+P)/5"), group = c("P","A","B","C","D","T")) senders_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique() receivers_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique() sce = sce[, SummarizedExperiment::colData(sce)[,celltype_id] %in% c(senders_oi, receivers_oi)...
I have a variable with two conditions. How to do an analysis of `Yes-No`, but not `No-Yes`? I want to avoid the redundant heatmap. ```R contrasts_oi = "'Yes-No'") contrast_tbl =...
Some results appear to be driven by a single sample or perhaps two. Could the prioritisation be made robust to such cases? 
Dear Saeyslab team, Thanks for the nice package! I have been running the analysis on multiple datasets using the following vignette: https://github.com/saeyslab/multinichenetr/blob/main/vignettes/condition_specific_celltype_MISC.knit.md As well as using the function: multi_nichenet_analysis I...
Depending on the order the analyst executes `library(nichenetr)` and `library(multinichenetr)`, ```r > combine_sender_receiver_de(celltype_de, celltype_de, senders_oi, receivers_oi, lr_network) Error in combine_sender_receiver_de(celltype_de, celltype_de, senders_oi, : unused argument (lr_network) ``` `multinichenetr::combine_sender_receiver_de` avoids the...
I noticed a potential namespace conflict with the `summarise` function. The code snippet below highlights where the conflict occurs: `abundance_df_summarized = abundance_df %>% mutate(keep = as.logical(keep)) %>% group_by(group_id, celltype_id) %>%...
