Tag: entrezID

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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Probe annotation file for microarray platform MoGene-1_0-st-v1

Hi, I would use the pre-built Bioconductor annotation databases / packages for this array (I have used this array a few times over the years): mogene10sttranscriptcluster.db mogene10stprobeset.db Most likely mogene10sttranscriptcluster.db is what you want: require(mogene10sttranscriptcluster.db) columns(mogene10sttranscriptcluster.db) [6] “ENTREZID” “ENZYME” “EVIDENCE” “EVIDENCEALL” “GENENAME” [11] “GO” “GOALL” “IPI” “MGI” “ONTOLOGY” [16] “ONTOLOGYALL”…

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What to do if the Entrez id that I have had been updated with a new one and now is associated with a gene

What to do if the Entrez id that I have had been updated with a new one and now is associated with a gene 0 For context, this is part of an RNAseq analysis, I have a list of genes, which was generated by annotateMyIDs using the Entrez id from…

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Community detection protocol and failed gene enrichment

My data is a file of about 19000 genes from a 100 patients. I tried to use these data to create a network by using igraph. Firstly, I had all the names of the genes converted to ENTREZID and from the 19000 genes I kept around 14000. Then I had…

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GO Enrichment Analysis in R

GO Enrichment Analysis in R – Count all the parents of each Term 0 Hi, I’m trying to implement a new GO tool in R. After I have a list of genes, I’m using the following code to retrieve the relevant annotation for each gene: library(AnnotationDbi) AnnotationDbi::select(org.Hs.eg.db, keys = genes.list,…

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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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[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi

[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi 1 Hello, I have microarray data from the chip [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], and I am trying to annotate the probe IDs in R using the hugene10sttranscriptcluster.db package and the following function:…

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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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