Tag: entrezID

Finding EntreZ IDs for refseq IDs

Finding EntreZ IDs for refseq IDs 1 Hi all, I have a list of bacterial RefSeq IDs corresponding to protein sequences (e.g., WP_007430823.1, WP_019686959.1, etc.). I need to retrieve the corresponding EntreZ IDs for these RefSeq IDs, in order to cotinue the RNA-seq downstream analysis (GO enrichment analysis ). Here’s…

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Error in CIBERSORTx

Hello, I am trying to use CIBERSORT to deconvolute the immune cells in pancreatic cancer after my treatments. I have 3 biological replicates of Control, Treatments A,B,C. Using edgeR, I created the cpm matrix which is not log transformed. and converted it to the required format as follows: # Load…

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tximport error: vroom

when i trying import a list of salmon counts files quant.sf: txi <- tximport(files=files, type=”salmon”, tx2gene=tx2gene[,c(“refseq”, “entrezid”)], countsFromAbundance=”lengthScaledTPM”) Rstudio throw me a error: reading in files with read_tsv 1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value why did it happen? Here are files…

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Network analysis with cytoscape

Network analysis with cytoscape 0 Hi Biostars, I try to use cytoscape on my RNA-seq data. After converting about 1000 DEGs into ENTREZID, I put the list into cytoscape and it makes a very complicated network. Could we use this tool to identify which gene/transcription factor is important from our…

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How to change from gene_id to GeneID/EntrezID using R

How to change from gene_id to GeneID/EntrezID using R 0 Hello im currently doing a differential expression analysis and the identifiers im using are gene_id’s, but to do the GO enrichment analysis and the domain anotation i need to have them in GeneID which according to what I have investigated…

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Hugo_Symbol to Entrez ID

Hello, I have Myeloid-Acute Myeloid Leukemia (AML) RNAseq data file data_mrna_seq_rpkm.csv. This file has Hugo_Symbols for all 22,844 genes but not its Entrez IDs. I was able use to two methods in R programming 1) library(org.Hs.eg.db) mapIDs method and 2) biomaRT method to get the entrez_ID of only 16,569 genes…

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DESeq2 results – Annotating and exporting results

Hi, I am working with isoforms.results from RSEM analysis. I am trying to annotate my deseq results with symbol and entrez IDs, following the vignette master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#annotating-and-exporting-results Unfortunately, I cannot export them as a csv file because the 2 elements I am adding are list. do you have any idea how…

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Converting gene id to entrez id with clusterprofiler

Converting gene id to entrez id with clusterprofiler 0 Hi, Im new to R and i’ve been trying to use clusterprofiler to convert my gene_ids to entrez_id for further analysis. I work on the msu7 rice genome and my gene ids looks like this (LOC_Os08g09610, LOC_Os06g05660). Since, it was a…

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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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converting Gene ID to GeneSymbols

converting Gene ID to GeneSymbols 0 Hello I am converting the geneids into Gene symbol using the map function. The conversion is going fine without any error but when I am checking online on ncbi website its showing a different symbol for that geneid . the following is the code…

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difference between mgeneSim and mgoSim

Hi everyone, I’m trying to use GoSemSim but I’m struggling due to his results. I started using mgeneSim function, and i passed an array of 11000+ EntrezID genes. It gave me a similarity matrix with some columns and rows all containing value “1”. I think is because, after mapping the…

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rna seq – building custom gtf file with entrez ID for any organism

How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf. My organism is canis_familaris I have to use is this source. How do I…

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How to extract genes of a specific GO-term/pathway

clusterprofiler: How to extract genes of a specific GO-term/pathway 2 I was wondering how to get the list of genes grouped in a particular GO-Term of Biological Pathway. I have an enrichGO output (using the clusterprofiler package). From this result, I’ve into a bar plot (see below). For example, my…

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Dot Plot using KEGG

Dot Plot using KEGG 2 Hi, I´m trying to do a dotplot using data from KEGG. I have my data represented, but I don´t want the species name in the X axis. My comand is: kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_organism = “mmu”…

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Converting RefSeq protein accession IDs into entreZ IDs

Converting RefSeq protein accession IDs into entreZ IDs 0 Hi, I have a list of genes with Refseq accession ids and I want to convert it to EntrezID, which can then be fit in the GENE ONTOLOGY enrichment and pathway analysis like DAVID and gProfile (these IDs belong to a…

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bitr() doesn’t recognize the keys I’ve entered as valid gene symbols for my organism’s database (‘SYMBOL’).

bitr() doesn’t recognize the keys I’ve entered as valid gene symbols for my organism’s database (‘SYMBOL’). 0 Hello, In trying to re-run my pathway analysis with a DEG set annotated with gene symbols. I have encountered this error while wanting to retrieve Entrez IDs for clusterProfiler. This is a new…

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A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package

A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package 0 Hello everyone, When I run the bitr command, I get warning message saying that 58.9% of input gene IDs are fail to map…, like the following: library(ggplot2) library(clusterProfiler) > gs.up =…

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Error in change Affymetrix transcript cluster id to Gene Symbol in microarray

Error in change Affymetrix transcript cluster id to Gene Symbol in microarray 0 annotLookup <- select(hugene20sttranscriptcluster.db, keys = “TC1000011370.hg.1” , keytype = “ENTREZID”, columns = c( “ENSEMBL”, “SYMBOL”, “ENTREZID”)) Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for ‘ENTREZID’. Please use the keys…

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TAIR Gene Symbols

Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…

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data file link: | Chegg.com

data file link: drive.google.com/file/d/1Odr12yDiUwI02-BfaXrHehKBM1uMW_1N/view?usp=share_link Step 1 (5pts) Load the file GSE124548.raw.txt into R and create a new dataframe with just the columns with the raw counts for healthy (HC) and CF patients before treatment (Base) and call it readcount. Use the first column (EntrezID) in the original file as the…

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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?

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”,…

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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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Error when using compareCluster from enichment

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…

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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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no gene can be mapped (RNAseq analysis)

gseKEGG – no gene can be mapped (RNAseq analysis) 0 Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms, it…

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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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org.Hs.eg.db gives more than one ENTREZID for a gene symbol

There is no way to specify the source of gene symbols for an OrgDb. For TEC, one comes from HGNC, and the other comes from OMIM. When we generate the OrgDb packages, we don’t distinguish between sources, as they are all (as far as NCBI is concerned) ‘real’ gene symbols….

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Error printing a CompressedGRangesList

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

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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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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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