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Tag: compareCluster
cluster analysis – The enrichWP function is no longer recognized in `comparecluster()` (clusterProfiler R package)
I have been using clusterProfiler for quite a while, specifically the compareCluster() function. I have used enrichKEGG()and enrichWP()for my workflow since January 2023. But now fun = “enrichWP” isn’t recognized in the comparecluster() function. Indeed when checking the R doc, it does now state for the fun argument : One…
Bioconductor – clusterProfiler
DOI: 10.18129/B9.bioc.clusterProfiler This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…
KCouper/Liverpool K-means RNAseq Analysis November 2020
R3 VAR14 vs RBC no TNF k-means q0.05 1. Genelist Selection groupsName<-“R3_VAR14_kmeans_q0.05” countsTable<-read.delim(“RNAseq2019July_5.txt”, header = TRUE, sep = “\t”,check.names=FALSE,row.names=1) head(countsTable) AllGeneNames<-countsTable$Gene_Symbol #head(AllGeneNames) tempA<-countsTable topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_0h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_0h))####find indexes listA<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_2h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_2h))####find indexes listB<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_6h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_6h))####find indexes listC<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_20h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_20h))####find indexes listD<-tempA[ topDEgenes,…
To draw a heatmap displaying DEGs associated with a specific KEGG pathway.
To draw a heatmap displaying DEGs associated with a specific KEGG pathway. 0 Hello, I hope all of you having a great day. I have difficulties drawing a heatmap displaying DEGs associated with a given KEGG pathway in R studio. I used to conduct enrichment analysis for KEGG pathways, using…
How to plot the result of compareCluster using ggplot
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?
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
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…
cluster profiler for pathway analysis in scRNA Seq
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…
Preventing overlap of gene labels/names in cnetplot
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…
How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?
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)…