Tag: enrichGO

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

clusterprofile enrichment analysis 1 Hello, Can I use clusterprofile enrichment functions like enrichGO() in case I have ensemblId and symbol(gene name) from old version GTF file (as they will not mapped or join with org.Hs.eg.db ). and which database can be passed for OrgDb param in enrich GO other that…

Performing GO analysis from Differential Peaks 0 Hello everyone, I called for FindMarkers() in order to find differential peaks between two biological conditions and the following was output (“diff.peaks”). My question is how would I generate a nice chart for GO analysis from this? My current code is: install.packages(“JASPAR2022”) library(JASPAR2022)…

Hello everyone, Initially I express that I am not very expert in bioinformatics analysis. I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. I select the data by calculating the zscore. Thanks to the tutorials and the forums I have managed…

Questions about DESeq and GOenrichment analysis for tomato 0 Hello all, I am a beginner for bioinformatics and I have 2 questions about RNAseq data processing for tomato. 1) I am always confused about the DESeq’s normalization function for gene length. I have 2 data sets at hand, one is…

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…

Hi! Apologies for the stupid question! but I think I am doing something wrong but i do not understand what. I would like to do ORA analysis on bulk-RNAseq dataset so I tried both clusterProfiler and also genekitr.` However, despite getting the same terms, but I have different p-adjusted value…

In several manuals (example) on ChIP-seq analysis they pre-select, for instance +1000bp and -1000bp from the TSS as the “promoter-bound” regions: peakAnno_bcl11b <- ChIPseeker::annotatePeak(peak = ‘bcl11b_peaks.narrowPeak’, TxDb=txdb, tssRegion=c(-1000, 1000) ) which produces an object with a slot @anno in which each peak is assigned either “Promoter”, “5’ UTR”, “3’ UTR”,…

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…

Hi, I’m doing an Over Representation Analysis using the clusterProfiler package. When I used the enrichGO function, I obtained a dataframe with the following columns: _ONTOLOGY: BP (in my case) _ID: GO ID. _Description: Description of the Biological Process. _GeneRatio: ratio of input genes that are annotated in a term….

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

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…

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…

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)…

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…