Tag: compareCluster

Hello, I am trying to plot the result of compareCluster. ck = compareCluster(geneCluster = data, fun = enrichGO, OrgDb = “org.At.tair.db”, keyType = “TAIR”, ont = “BP”, pAdjustMethod = “BH”, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable = TRUE) After this code, I get the result, but there is another…

Is the same order when using p value or q value for compareCluster analysis? 1 Hey, I’m so confused about a simple question, hope you guys could help me! So I do a GO analysis using compareCluster as I compared my downregulated genes and upregulated genes. I’m wondering whether the…

Error when using compareCluster from enichment 0 I have two data frames of RNA translated to the Entrezid Ids and when running the chunks through compare cluster I get the following error: Error in $<-.data.frame(*tmp*, “Cluster”, value = integer(0)) : replacement has 0 rows, data has 120 The data is…

Dear Community, I am trying to show pathway expression in 6 clusters that I identified in disease and control and would like to compare the corresponding clusters. I followed this post 438466 and used Pratik ‘s solution. Which gives me a plot only for the disease. However, I would like…

Hello, I’m working on creating a cnetplot based off of a compareCluster enrichment result. I want to plot 5 GO Biological Processes as the individual categories with the corresponding genes connecting with each one of them. I’m able to do this successfully with the cnetplot function, but since each category…

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…