Tag: gseGO

No genes mapped in clusterprofiler gseGO

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

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No gene can be mapped

Hi When I do my data’s Gene Set Enrichment Analysis with ClusterProfiler using codes of Mohammed Khalfan from website, when I run the following code and got the error message. gse <- gseGO(geneList=gene_list, ont = “ALL”, keyType = “ENSEMBL”, nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff =…

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Errors in Functional Enrichment Analysis with Clusterprofiler

Errors in Functional Enrichment Analysis with Clusterprofiler 0 library(clusterProfiler)library(org.Hs.eg.db) library(tidyverse) library(DOSE) library(ReactomePA) library(enrichplot) library(fgsea) library(data.table) library(ggplot2) keytypes(org.Hs.eg.db) res = read.csv(“coex.Csv”) head(res) original_gene_list = res$correlation names(original_gene_list) <- res$gene gene_list<-na.omit(original_gene_list) gene_list = sort(gene_list, decreasing = TRUE) gse <- gseGO(geneList=gene_list, ont =”ALL”, keyType = “ENSEMBL”, minGSSize = 3, maxGSSize = 800, pvalueCutoff =…

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Which function is best for pathway analysis?

Which function is best for pathway analysis? 1 Hi Biostars, I found there are many function to perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO() which made me quite confuse which result I should focus on. Getting a correct background gene set is important. However, how can we find…

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GO ENRICHMENT ANALYSIS- DESEQ

I keep getting this Error message: preparing geneSet collections… –> Expected input gene ID: C9orf78,CNOT9,SPIDR,FAM9B,SDC1,CCDC182 Error in check_gene_id(geneList, geneSets) : –> No gene can be mapped…. Here is my code, i attempting to perform gene set enrichement analysis: GroupA <- results(dds, name = "Cancer_Type_healthy_vs_MESO") original_gene_list <- GroupA$log2FoldChange names(original_gene_list) <- GroupA$X…

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Find potential important genes from bulk-RNA seq experiment

Find potential important genes from bulk-RNA seq experiment 0 Hi Biostars, After finding DEG genes, I try to find important genes that may cause for a disease so I do pathway analysis with GSEA and find pathway with highest enrichment score using gseKEGG() and gseGO(). Is that genes in the…

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Ensembl site unresponsive in clusterProfiler analyses

Ensembl site unresponsive in clusterProfiler analyses 0 Hi, thanks for all the useful work. I’m writing to ask about an issue I’ve recently encountered with clusterProfiler in its latest version. I’m trying to implement an approach using parallel::mclapply and some clusterProfiler functions (e.g. groupGO, enrichGO, gseGO) to process few sets…

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gseGO() –> No gene can be mapped

Dear all, I have a list of S. cerevisiae genes and I want to do GO enrichment analysis using clusterProfiler. I already obtained some information using enrichGO() and groupGO(), and I want to see what I can obtain with gseGO(). I use the package org.Sc.sgd.db as my organism database. Here…

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How to Load a Molecular Signature Database into clusterProfiler gseGO?

How to Load a Molecular Signature Database into clusterProfiler gseGO? 0 I am using gseGO this way: gse <- gseGO(geneList=gene_list, ont =”ALL”, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = org.Hs.eg.db, pAdjustMethod = “fdr”) Let’s say I want to analyze against a molecular signature…

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could not find function “gseGO” in ClusterProfiler

could not find function “gseGO” in ClusterProfiler 1 I am trying to run the code using the example data set, gse <- gseGO(geneList=gene_list, ont =”ALL”, keyType = “ENSEMBL”, nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = org.Dm.eg.db, pAdjustMethod = “none”) however…

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go analysis result error

Hello everyone in biostars. I’m trying to do a go, kegg analysis. But I’m having an error. I’m using the following code. reference from github library(AnnotationHub) ah <- AnnotationHub() query(ah,’Oryza_sativa’) rice <- ah[[‘AH107684’]] rice library(clusterProfiler) setwd(“C:/Users/R”) deseqas <- read.csv(‘deg.csv’) as <- deseqas$gene geneList = sort(as, decreasing = TRUE) IDtable <-…

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How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header?

How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header? 0 BiocManager::install(“clusterProfiler”, version = “3.16”) BiocManager::install(“pathview”) BiocManager::install(“enrichplot”) library(clusterProfiler) library(enrichplot) # we use ggplot2 to add x axis labels (ex: ridgeplot) library(ggplot2) # reading in data from deseq2…

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Phenotypic plasticity and genetic control in colorectal cancer evolution

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

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FindMarkers for ClusterProfiler

FindMarkers for ClusterProfiler 1 Hi, I recently ran FindMarkers to compare DEG between two different clusters in a single-cell RNA-seq analysis This is my code: markers= FindMarkers(obj, ident.1=c(4), ident.2 = c(5)) head(markers) dim(markers) table(markers$avg_log2FC > 0) table(markers4v5$p_val_adj < 0.05 & markers$avg_log2FC > 0) I would like to run ClusterProfiler to…

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