Questions tagged [gsea]

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fgsea returns an empty data frame - How to solve?

I am trying to run fgsea on a vector, v, containing Pearson's correlation. The vector names contain the corresponding gene IDs. When I run the following command, I get back an empty dataframe. ...
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1answer
17 views

Can I use GSEA to look for enrichment in data that is grouped into sets but are not necessarily genes?

I have yeast growth data in various experimental conditions that are classified by the strain type. Can I use the GSEA tool from the Broad Institute to test for enrichment of specific groups of ...
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8 views

Cannot use .owl files downloaded in PANTHER with paxtoolsr functions

I am trying to transform a PANTHER pathway into a GSEA-appropriate format. For this, I am trying to execute the following code taken from paxtoolsr documentation ...
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2answers
278 views

GSEA - Gene Set Enrichment Analysis - in R studio

I have been trying to conduct a classic GSEA using the broad institute software and can not figure out how to compile it in R for the life of me. I am aware that there exists other packages in R that ...
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73 views

Question about enrichment score (ES) and NES from GSEA

I have two results from separated two GSEA runs, and i want to know which sample has the most enrichment about specific pathway (gene set). Can I use ES (or NES) from two different GSEA analysis ...
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1answer
99 views

I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application

I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would ...
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122 views

I am getting a parsing error when uploading .chip file to GSEA software

I get the following error when I try to load a .chip file to GSEA software. What is the problem? ...
4
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1answer
148 views

Gene Ranking - signal to noise ratio used in GSEA-P algorithm?

I'm looking at Broad Institute's orignal GSEA-P algorithm R script which I downloaded here: http://software.broadinstitute.org/gsea/downloads.jsp. I'm trying to adapt their GSEA.1.0.R script to ...
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3answers
753 views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
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3answers
3k views

Script to allow gene set enrichment analysis of 10x genomics data in R

I have 10x single cell RNA seq data. Which R package is best suited for analysis of the 10x data matrix. What is the script to prepare the data for downstream GSEA analysis. I have already processed ...
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1answer
48 views

Retrieving gene matrix from internet in GSEA desktop

This error appeared to me, and I have the program connected to the internet. I already installed java 8, but it still doesn't get me the gene set databases.
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1answer
257 views

GSEA- parsing error for .cls file

I am creating a .cls file for my GSEA analysis and see the below error. Can anyone suggest a solution? I create the file using TeXworks. The file looks like this: ...
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2answers
51 views

Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

As the question states, I am interested in an analysis similar to Gene Set Enrichment Analysis (ranked gene sets) but focused on locus-level data instead of genes. To explain in greater detail: I ...
8
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1answer
322 views

Comparison of gene set enrichment statistics

I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
5
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2answers
143 views

Clarification on Gene Enrichment

When I run a GSEA analysis on two conditions from the same RNaseq (negative control PBS injection VS positive control CpG injection) from the same dataset/same gene list, I get results that look ...
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3answers
240 views

How to adapt the fgseaL function to perform rapidGSEA computation of gene ranks across 9 different phenotype labels?

I wish to adapt the r language function fgseaL, https://github.com/ctlab/fgsea , to perform rapidGSEA, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1244-x , computation of ...