Questions tagged [gsea]

Question 1

GSEA by broad institute is really a powerful tool to handle this analysis very efficiently compared to other packages such as clusterProfiler. Specially it comes with the MsigDB curated genesets for 3 ...

Question 2

I've been using pathway analysis methods like GSEA and GSVA, which evaluate pathway activity based on gene expression levels. However, these methods seem to assume that the more highly expressed a ...

Question 3

New to bioinformatics, interested in kidney cancer. I'm trying to repeat the findings from a paper I like (https://www.nature.com/articles/s41467-021-21068-9). They used the TCGA KIRC, TCGA KIRP, and ...

Question 4

I've made my files for a GSEA ANALYSIS, but the software gives me this error: ...

Question 5

I'm having some major chaos with the output table generated and then passing that to my plot function. New to this (1st time), could somebody review this piece of code and suggest some corrections. I ...

Question 6

(For context: I'm somewhat new to bioinformatic analyses but am mostly comfortable with R) I have identified transcriptomically and morphologically different cancer cell populations within a patient (...

Question 7

Trying to understand when GSEA is more appropriate than GSVA and vice versa. I have seen cases when running GSEA and GSVA on the same task - compare enrichment of a geneset between two groups - gives ...

Question 8

I need to plot the results of a GSEA analysis we performed on scRNA data. I am stumbling upon various possibilities for this and sometimes I am struggling a bit to understand how to interpret it. My ...

Question 9

I'm want to perform an GSEA of some RNA-seq data but when I upload the expression data set file this problem appears but I don't know how to solve it. Thanks for your help. Pol Error Details ...

Question 10

I have a gene set containing a set of 1500 genes in which I did differential gene expression using limma voom pipeline. After this step I wanted to analyze a specific set of pathways the metabolism ...

Question 11

I haven't found any relevant posts, so here is my question (it's more a question on statistics I believe): I have the deseq2 output of DE genes( around 25000 genes) , and among them 1000 are ...

Question 12

I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...

Question 13

I built the matrix as the gmt example in https://docs.gsea-msigdb.org/#GSEA/Data_Formats/ but It still has errors when I try to run it. When I try the gene set from https://www.gsea-msigdb.org/gsea/...

Question 14

I have a data frame columns are pathways and genes are rows Like ...

Question 15

I want to check the correlation between the expression of a given "test_gene"* in each cluster within a scRNA-seq database with the expression of a signature (i.e., gene sets whose ...

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Questions tagged [gsea]

How to efficiently rank the genes in a transcriptome dataset by signal2noise ratio?

How Can Pathway Analysis Methods Account for Genes with Different Activation Roles?

Performing GSEA on TCGA and NES signs are flipped

Error in Load Data in GSEA 4.3.3

Trying to plot the results of GSEA in python

How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

GSEA vs GSVA: Pros and cons of each method

GSEA results plot interpretation

Error in GSEA expresion data set file

Pathway Enrichment Analysis for one specific pathway?

enrichment of DE genes within wide regions not pathways, hypergeometric test or GSEA?

Gene Set Comparison Without Expression Data

Run gmt format download from GSEA

Making a list of lists in R

Correlate ssGSEA score with Seurat's scaled expression data

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