Tag: gsekegg

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”…

I am trying to use the gseKEGG function in the R package clusterProfiler with the KEGG database entries for Streptomyces coelicolor. This code snippet confirms that KEGG supports this organism, with kegg_code of ‘sco’. search_kegg_organism(‘sco’, by=’kegg_code’) returns kegg_code scientific_name common_name 2810 scon Streptococcus constellatus subsp. pharyngis C232 <NA> 2811 scos…

I’ve got a csv file with 2 columns – one of Entrez IDs and another of gene’s measurement/fold-change. I am running code trying to use gseKEGG(), getting the gene list prepared for that function like this: d <-fread(“file.csv”) geneList <- d[,2] names(geneList) <- as.character(d[,1]) geneList <- sort(geneList, decreasing = TRUE)…

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…

Issues with clusterProfiler and WikiPathways 0 Hello, are there any known issues with WikiPathways-related functions in clusterProfiler v. 4.0.5? I’m not able to retrieve even the list of supported organism using the get_wp_organisms() because I’m returned with: “Error in file(con, “r”) : cannot open the connection”. I had experienced similar…

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…

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