hdWGCNA
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smorabit
High dimensional weighted gene co-expression network analysis
Hello, thank you for the great package! By default, PlotDMEsLollipop arranges modules based on their Avg.log2(Fold Change) values. Is there a way to arrange the modules in numerical order instead?
In Seurat V5 using hdWGCNA, I encountered the following issue: 'Error in UseMethod(generic = "JoinLayers", object = object) : no applicable method for 'JoinLayers' applied to an object of class...
Hi @smorabit, I would like to know if it is possible to use hdwgcna with single Cell ATAC coverage data instead of the SC RNA-seq expression matrix. How should the...
When I try to construct metacells in each group, I meet the error below. ``` > unique(seurat_obj@misc[["tutorial"]][["wgcna_metacell_obj"]]@meta.data$cell_type) [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" > seurat_obj
Hello, Thanks for your effort and maintenance of the package! I am using your pipeline for hdWGCNA with pseudobulk data and am running into a problem with the ConstructPseudobulk function....
Hi, I'm trying to check one trait (treatment vs control) against the MEs to figure out which modules show strong correlation with the trait. When I try this code: seurat_obj$group1
Hey Sam, big fan of hdWGCNA. Thanks for continously maintaining it! In the latest dev version (0.4.00, @[9b2e71a](https://github.com/smorabit/hdWGCNA/commit/9b2e71abd0eb5ffd89ca16e8898b915928502f8a)), calling `MetaspotsByGroups` fails due to an error in `ConstructMetaspots`. The function argument...
# question Hi @smorabit ,thanks for your convenient tool! After `PlotKMEs`, I wonder whether the gene symbols on the right side are in the opposite order compared with the original...
Hi, I'm trying to use the MetaspotsByGroups function with multiple variables from meta.data, including "case," "batch," "region," and "distance." However, when I include the "distance" variable, I encounter an error...
Let's assume that we already have a metacell assignment for the cells, e.g., in the form of a vector. Is it possible to use this assignment such that hdWGCNA creates...
