Tag: enrichkegg

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…

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Enrichment dotplot color

Enrichment dotplot color 0 Hi, I have a question about enrichGO or enrichKEGG dotplot. The dotplot I drew when using enrichGO() or enrichKEGG() was this color: But when I repainted it today it turned into this color: And I can’t change it back, can anyone help me get it back…

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enrichKEGG function error

enrichKEGG function error 1 @d4a334e3 Last seen 4 hours ago Germany Hello, I was trying to check kegg enrichment analysis for my Bulk RNAseq DGE results, and I am getting this error –> No gene can be mapped…. –> Expected input gene ID:–> return NULL… could you kindly tell what…

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KEGG enrichment in R and gene IDs

KEGG enrichment in R and gene IDs 2 @239caad3 Last seen 3 days ago Belgium Hi, I am trying to run a KEGG enrichment analysis on my data. My genes are in SYMBOL, which I converted to ENTREZID, but I need them in “kegg” or “ncbi-geneID” to run enrichKEGG. I…

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CluserProfiler message “No gene can be mapped”

Hi Biostar users, I am working with clusterprofiler enrichKegg function KEGG_all = enrichKEGG(regulated.gene$entrez, organism=”human”) I have used library(org.Hs.eg.db) to convert gene names(Symbols) to Entrez ID which is the possible input to use this function. However I am seeing strange message and I am not sure what could be the reason?…

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Enrichment analysis based on kegg for zebrafish

Hello There! I am doing the enrichment analysis based on kegg. The analysis is based on zebrafish entrezid/ncbi-geneid Clusterprofiler seems to work for this example. data(geneList, package=”DOSE”) de <- names(geneList)[1:100] yy <- enrichKEGG(de, pvalueCutoff=0.01) head(yy) But when I tried my code, it does not work. I did it for my…

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Problem with universe argument in enrichKEGG

Problem with universe argument in enrichKEGG 0 Hi all, I am trying to do KEGG enrichment with enrichKEGG, I was wondering if I need to specify universe argument. Could you please help me with it? In the documentation, it says “universe: background genes. If missing, the all genes listed in…

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clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis

Hi there! I would like to perform KEGG enrichment with some differentially expressed gene data from RNAseq data. I am working on a non-model organism. I have 1) KEGG to GeneName Mapping head(expr5_FS_final) KEGG unigene_FS 1 K02727 FS_gene_1 2 K17277 FS_gene_3 3 K17307 FS_gene_10 4 K14453 FS_gene_11 5 K14700 FS_gene_11…

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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…

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Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

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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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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)…

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How to colour points in cnetplot of clustprofiler?

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…

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What’s the difference between enrichKEGG and gseKEGG

What’s the difference between enrichKEGG and gseKEGG 3 Hi, I was wondering what is the difference between enrichKEGG and gseKEGG in R package ClusterProfile. Thanks! clusterprofiler KEGG • 2.3k views Source link

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