Tag: enrichGO

Cnet plot showing non-significant genes within pathway

Hi All, I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from…

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Cluster Profiler output not the same as Enrichr output

Cluster Profiler output not the same as Enrichr output 0 @angkoo-23537 Last seen 18 hours ago United Kingdom Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021…

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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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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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