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…

Continue Reading cluster analysis – The enrichWP function is no longer recognized in `comparecluster()` (clusterProfiler R package)

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…

Continue Reading Bioconductor – clusterProfiler

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,…

Continue Reading KCouper/Liverpool K-means RNAseq Analysis November 2020

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…

Continue Reading To draw a heatmap displaying DEGs associated with a specific KEGG pathway.

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…

Continue Reading How to plot the result of compareCluster using ggplot

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…

Continue Reading Is the same order when using p value or q value for compareCluster analysis?

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…

Continue Reading Error when using compareCluster from enichment

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…

Continue Reading cluster profiler for pathway analysis in scRNA Seq

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…

Continue Reading Preventing overlap of gene labels/names in cnetplot

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)…

Continue Reading How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?