Bioconductor Forum

Hi, I'm curious if anyone has tried to clone or fork the fgsea package on the latest version of R? How can I reproduce the scripts to run locally

fgsea

updated 8 months ago • yimjohns

Hello all, I was trying to perform GSEA for a dataset using the `fgsea` R package. The code I used was `fgseaRes <- fgsea(pathways = pathways, stats = ranks, minSize = 5, maxSize = Inf)` I received an warning

fgsea

updated 3.6 years ago • zli1

Running into an error of not being able to install or run fgsea in R Version 1.4.1106. ``` # library(fgsea) Error: package or namespace load failed for ‘fgsea’ in loadNamespace(i, c(lib.loc, .libPaths...vI[[i]]): there is no package called ‘fastmatch’ In addition: Warning message: package ‘fgsea’ was built under R version 4.1.1 #install.packages("fgsea", repos="http://cran.rstudio.com/"…

r fgsea

updated 2.9 years ago • amir.khan

Hi everyone I dont really have problems running fgsea itself but im trying to understand what gseaparam argument in fgsea() means. The vignette says it's a GSEA weight parameter...but weightage of what? each fgsea term? and to what exactly hope to hear some clarifications; tried googling it's still not clear to me

fgsea

updated 4.5 years ago • kavator

Hi All i ran fgsea() successfully; my sample is brain tissue but im getting quite a few fgsea GO hits that describe other relatively far off...tissues processes -like digestive system.. etc. i was wondering if there's a possibility to run my fgsea just on brain related GO processes? would appreciate any advice

fgsea

updated 2.1 years ago • kavator

Hi all, fgseaRes <- fgsea(pathways = c2_list, stats = stats, minSize=15, maxSize=500) significantResults <- fgseaRes[fgseaRes$padj < 0.25, ] The significantResults

fgsea

updated 7 months ago • Chris

Hello everyone, Back in October I performed fgsea analysis without problem, obtaining up/downregulated genesets. Now I am trying to do another analysis with fgsea, and...msigdbr_list <- split(x = msig$gene_symbol, f = msig$gs_name) #Running fgsea algorithm: fgseaRes <- fgseaMultilevel(pathways = msigdbr_list, stats = ranks) R version 4.1.3 (2022-03-10…

fgsea

updated 2.7 years ago • Barista

I can use GSEA to compare two datasets ([link to GSEA FAQ on how to do this][1]). I found `fgsea` package that can do GSEA calculation with pathways but I cannot figure out how to use this package to do the two datasets

GSEA fgsea

updated 17 months ago • Cen

Hi, I'm trying out the `` fgsea `` package, which is a great improvement over other much slower `` gsea `` implementations.   One question though - I'm interested...code> data(examplePathways)<br/>   data(exampleRanks)</code> <code>  fgseaDnRes <- fgsea(pathways = examplePathways,stats = exampleRanks,minSize=15,maxSize=500,nperm=10000)&l…

fgsea gsea

updated 7.9 years ago • rubi

I have been trying to follow the tutorial posted on "https://stephenturner.github.io/deseq-to-fgsea/#load_some_results_from_deseq2" I had used the using FGSEA package on, "https://bioconductor.org/packages/release/bioc

fgsea rna

updated 10 months ago • Gordon

Hi,   Does fgsea order the stats argument? What I'm currently doing is order ordering the effect (i.e. log treatment vs. control fold...changes) but their p-vaiues and passing that to fgsea. But the fgsea code suggests it re-ranks stats so the p-value ranking is lost. Is that the case? and if so is there any way to

fgsea

updated 7.5 years ago • rubi

biocLite command and am currently running it in R version 3.3.3 “Another Canoe.” When running the fgsea command the algorithm runs quickly (less than 1 second) for any number of permutations less than 1000, only taking 1.46

fgsea gsea

updated 7.4 years ago • shawn.w.foley

results table with such metrics with LFC, p.adf (or FDR) and etc. I wonder should I use in fgsea analysis all genes with estimated LFC values (from results table) or is it better to restrict set by p.adj (or FDR) < 0.05

fgsea

updated 3.8 years ago • alexandr.gopanenko

how does shrinking affects those values in stat column Additionally; i dont get why does fgsea uses stat column (whose values are presumably not affected by lfc shrink) instead of a shrunken column of values

fgsea DESeq2

updated 3.8 years ago • kavator

Hi there guys. I have gene expression data collected from nCounter with a panel of around 700 genes (Pancancer immune profiling panel). I performed differential expression analysis and now I want to see which immune-related pathways are over or under expressed in my samples. In my nCounter samples I do not have normal tissue so I can´t perform a differential expression analysis between tumor an…

NanoStringDiff clusterProfiler fgsea

updated 19 months ago • pg45863

I try to run an fgsea analyses. So I create my own database looks like this : df_db <- read.csv('pathway_ecnumber.csv',sep=",") df_db path:map00010...pathways, stats, minSize, maxSize, gseaParam, : There are duplicate gene names, fgsea may produce unexpected results. The second warning I try to resolve with this line but it is not working : df_database

R fgsea

updated 3.6 years ago • julie.hardy

variation analysis. Robert (the creator of GSVA tool which I tried on my data) suggested me using fgsea because my data doesn't have differential express genes. However, fgsea requires differential express genes as input

fgsea

updated 7 months ago • Chris

S2N metric implemented in GSEA (I just wrote a function to perform this for me and feed it into fgsea). I got everything to work but I'm trying to ensure what I see is actually real. Please see the image below as a representative

fgsea gsea sc-rnaseq

updated 6.4 years ago • atakanekiz

Part of the input for Gene Set Enrichment Analysis with [fgseaMultilevel](https://rdrr.io/bioc/fgsea/man/fgseaMultilevel.html) is a list of GO terms and genes assigned to it. E.g.: ``` library(fgsea) data(examplePathways) examplePathways...all of the ancestor terms. This means that data retrieved from biomart is not immediately usable for `fgsea`. Here's an example: At first impression…

biomaRt GO ensembldb fgsea

updated 2.2 years ago • dario.beraldi

Hi all, I am trying to create GSEA and FGSEA for C57BL/6J Mice species. I had created a code for human species, and thought to switch out all human input as mice. However

gsea mice org.Mm.eg.db

updated 8 weeks ago • Gordon

I'm running `fgsea` on a single-cell data set with seven clusters. ```r markers_export0.2.res_0.2$cluster |> table() ``` 0 1 2 3 4 5 6 2318 713 1380...I'm running `fgsea` on a single-cell data set with seven clusters. ```r markers_export0.2.res_0.2$cluster |> table() ``` 0 1 2 3 4 5 6 2318 713 1380 1228...p_val_ad…

GSEABase fgsea msigdb GeneSetEnrichment

updated 3 months ago • Assa Yeroslaviz

pathway meaning the pathway has genes enriched that are down in treatment vs control? Also, does fgsea re rank the pre ranked vector I supply it? If it does, what is the benefit of supplying it a pre ranked vector? I appreciate

fgsea

updated 8 months ago • sropri

I try to run the example of fgsea package with R version 4.0.2 : ```r data(examplePathways) data(exampleRanks) typeof(examplePathways) fgseaRes <- fgsea...I try to run the example of fgsea package with R version 4.0.2 : ```r data(examplePathways) data(exampleRanks) typeof(examplePathways) fgseaRes <- fgsea(pathways = examplePathways, stats = example…

fgsea fgse

updated 3.6 years ago • julie.hardy

Hi all, I try to make plot as the tutorial using the same code: stats <- with(results, setNames(logFC, row.names(results))) fgseaRes <- fgsea(pathways = c2_list, stats = stats, minSize=15, maxSize=500) topPathwaysUp <- fgseaRes[ES > 0][head(order(pval), n=10), pathway] topPathwaysDown...code: stats <- with(results, setN…

fgsea

updated 7 months ago • Chris

which pathways different between them. I ran gene set variation analysis follow up with limma, fgsea, camera. enrichGO() also rank the pathway but we can't choose which gene set we want to analyze. Each of them gives different...Gordon comment on this post https://support.bioconductor.org/p/9158100/#9158140, seem p valule from fgsea is not truly significant as it is. When I search camera limma on…

fgsea GSVA CAMERA

updated 7 months ago • Chris

gt;% distinct() %>% group_by(SYMBOL) %>% summarize(stat=mean(stat)) res2 library(fgsea) ranks <- deframe(res2) head(ranks, 50) pathways.hallmark <- gmtPathways("human.gmt") pathways.hallmark %>% head() %>% lapply...head) fgseaRes <- fgsea(pathways=pathways.hallmark, stats=ranks, eps=0) fgseaResTidy <- fgseaRes %>% as_…

fgsea gsea

updated 9 months ago • Gordon

Recently, I have seen a post about `fgsea` for gene set enrichment analysis. In this [DESeq results to pathways in 60 Seconds with the fgsea package][1]. In this post...How to get the t-statistic using edgeR package? [1]: https://stephenturner.github.io/deseq-to-fgsea

r edger t-statistic fgsea gsea

updated 5.6 years ago • Biologist

implement functions for a Gene Set (Enrichment) Analysis, some of them are limma, gsar, gsva, piano, fgsea, pgsea. However I couldn't find an agreement for those tests which accept any statistic as input: `` fgsea ``, `` runGSA ``, `` geneSetTest

gsea concept gsa

updated 7.9 years ago • Lluís Revilla Sancho

finish computation. When I manually stop it I get the error message: <pre> Warning message: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : There are duplicate gene names, fgsea may produce

reactomepa reactome gsea fgsea

updated 6.5 years ago • martin.busch

nbsp; I tried to install "Chipseeker" on Linux CentOS7. but the problem occured. it said that "fgsea, DOSE, chipseeker had non-zero status exit".   is the package, Chipseeker undecent on Linux

Bioconduct or Chipseeker CentOS7 Linux installation

updated 8.1 years ago • spsp9987

Hi Is it possible to run ViSEAGO with results obtained by the ``fora`` function of the fgsea package? More specifically, I want to cluster the significant pathways from ```fora``` by semantic similarity. My ultimate

ViSEAGO

updated 3.7 years ago • tim.meese

my differential gene expression analysis. If I understand it correctly, `clusterProfiler::GSEA` uses `fgsea` under the hood to estimate significance levels and for that, it permutates the **gene labels**. However, if I remember correctly

clusterProfiler GSEA fgsea

updated 2.0 years ago • nhaus

Hi everyone; just want to double check my understanding of leading Edges in fgsea; according to FAQ of original gsea > "For a positive ES (such as the one shown here), the leading edge > subset is the set...Hi everyone; just want to double check my understanding of leading Edges in fgsea; according to FAQ of original gsea > "For a positive ES (such as the one shown…

fgsea

updated 4.5 years ago • kavator

We do not recommend using nPerm parameter incurrent and future releases > 2: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : > You are trying to run fgseaSimple. It is recommended...use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm > argument in the fgsea function call

clusterprofiler

updated 4.5 years ago • sunnykevin97

I have a query regarding the analysis of GSEA Results. For GSEA, I have used "fgsea" R package to obtain the dysregulated KEGG pathways. Now, I want to rank the dysregulated KEGG pathways. I have seen people

fgsea log2FC

updated 5 months ago • V_Vibes

changes generated by apeglm as the test statistic for gene set enrichment analyses when running the fgsea package. I have seen a paper that suggests the absolute value of Signal-To-Noise is a better metric than LFC: https://bmcbioinformatics.biomedcentral.com

apeglm fgsea Signal-To-Noise Ratio

updated 5.6 years ago • coulsonr

Novice here, this was a warning that I came across while running fgsea, which resulted in the final GSEA plot missing some bars. my question is, how best should i "normalize" my log2FC statistic

fgsea

updated 4 months ago • Danté

But it comes out the error. Thank you in advance for great help! Best, Yue > library(fgsea) > library(tidyverse) > library(data.table) > library(ggplot2) > setwd("/media/hp/04c65089-71ff-4b33-9a30-c21b8c77eda2...gt; pathways.kegg<- gmtPathways("c2.cp.kegg.v7.2.symbols.gmt") > fgseaRes_kegg<- fgsea(pathways = pa…

fgsea

updated 3.8 years ago • yueli7

and GSEA. Then we paste the results into a file that we can save as a CSV file ```{r} library(fgsea) library(enrichR) library(clusterProfiler) library(dplyr) genes <- data.frame(d$log2FoldChange, d$symbol) names(genes...lt;- d$symbol genes <- genes %>% dplyr::arrange(desc(d.log2FoldChange)) library(fgsea) library(enrichR) library(clusterProfiler) em <- enricher(gene…

clusterProfiler

updated 2.1 years ago • Rob

I have been using voom+limma+sva to analyse my RNA-Seq data of leukaemia. After some clustering analysis and prior knowledge to the data set, I now am trying to compare some of the samples in a group with the remaining data set. I used fgseaMultilevel() from fgsea package and did a pre-ranked GSEA using log(fold change) as the ranking matrix. However, as it is RNA-Seq data, I actually want...t…

limma deseq2 seqgsea sva deseq

updated 5.5 years ago • kentfung

I'm interested in this because, from what I have read, the stat column is useful for GSEA analysis (fGSEA package) and from what I have found and is posted in the vignette I get the impression it is best to use shrinkage for downstream

deseq2 stat lfcshrink

updated 4.7 years ago • divercory

2 Homo sapiens: Interleukin-6 signaling 1059683</code> As this behavior breaks build of my package (fgsea) and I need to fix it, I wonder is this transition final? If yes, may be it's better to remove organism specific prefix whatsoever

reactome.db fgsea

updated 7.7 years ago • assaron

nbsp;  verbose = TRUE,      seed = FALSE,      by = "fgsea") " \#\# <pre> preparing geneSet collections... --> Expected input gene ID: 94094,223650,17926,12831,29875,68178 Error in check_gene_id

GSEA clusterProfiler

updated 7.1 years ago • giuseppe0525

OrgDb = "org.Hs.eg.db", ont = "BP", keyType = "SYMBOL", pAdjustMethod="none") using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections... GSEA analysis... no term enriched...OrgDb = "org.Mm.eg.db", ont = "BP", keyType = "SYMBOL", pAdjustMethod="none") using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet coll…

clusterProfiler

updated 6 months ago • sawa

organism in the form of `.gmt` file, which is very useful for gene set enrichment tools like `fgsea`. Coming back to use the code a year later, I discovered that `keggGet` command started to fail when trying to retrieve modules

keggrest software error pathways modules kegg

updated 4.7 years ago • predeus

results$logFC, results$gene_symbol) # pathways is a list of gene vectors from msigdb fgsea_res <- fgsea(pathways=pathways, stats=stats, minSize=6, maxSize=300, nproc=8) nrow(fgsea_res[padj < 0.001 ]) # 137 hits at this stringency...do GSEA stats <- setNames(results_rand$logFC, results_rand$gene_symbol) fgsea_res_rand <- fgsea(pathways=pathways, stats=stats, minSi…

fgsea edgeR

updated 7 months ago • gene_bioconductor

Hi, I am running gene set enrichment analysis on R using the `fgsea` package and plotting the results using `ggplot`. The main code for plotting the results is as follows: ``` ggplot(fgseaRes_sig

ggplot

updated 3.0 years ago • nattzy94

nbsp;verbose = TRUE,       seed = FALSE,       by = "fgsea")_   3. However, I run the gseaplot() function with another gsearesults object derived from gsekegg() function..._data = FALSE,         seed = FALSE,      &nbs…

gsea clusterprofiler

updated 7.1 years ago • giuseppe0525

Dear Bioconductor admin, I am working on data analysis for microarray data, but I could not install into my R studio, Could you please help to solve my issue that How to install "maEndToEnd" into R studio in my Macbook? Thank you very much Here is the problem report from my screen: ``` > library(devtools) > library(remotes) > remotes::install_github("b-klaus/…

microarray maEndToEnd

updated 5.2 years ago • Jack

pvalueCutoff = 0.05, verbose = TRUE, OrgDb = organism, by = "fgsea", pAdjustMethod = "none") require(DOSE) library(enrichplot) library(DOSE) edo2dot <- gseDO(sorted_dfx) #barplot(gse, showCategory

clusterProfiler enrichplot clusterpro doseR dose

updated 2.4 years ago • rama

71), bit(v.1.1-14), Formula(v.1.2-3), AnnotationForge(v.1.22.2), htmlwidgets(v.1.3), httr(v.1.3.1), fgsea(v.1.6.0), acepack(v.1.4.1), pkgconfig(v.2.0.2), XML(v.3.98-1.16), farver(v.1.0), nnet(v.7.3-12), locfit(v.1.5-9.1), labeling(v.0.3

diffbind

updated 5.9 years ago • avantika6194

nbsp;   RSQLite\_1.0.0        stringi\_1.1.2        fgsea\_1.0.2          GO.db\_3.4.0          \[36\] scales\_0.4.1         stats4\_3.3.2

clusterprofiler

updated 8.1 years ago • Marcus

packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES' Old packages: 'AnnotationHub', 'curl', 'fgsea', 'GenomicAlignments', 'GenomicRanges', 'GOSemSim', 'IRanges', 'limma', 'Rsamtools', 'S4Vectors',   'VariantAnnotation', 'XVector

deseq2 DESeqDataSetFromMatrix

updated 7.4 years ago • zxy5139

nbsp;    rvcheck\_0.0.9       gridExtra\_2.3 \[19\] fgsea\_1.4.0         stringr\_1.2.0       tidyselect\_0.2.3 \[22\] autoinst

clusterProfiler GO GO enrichment genesetenrichment

updated 7.0 years ago • Huang, Lei [BSD] - CRI

rgl) library(tradeSeq) library(bioc2020trajectories) library(pheatmap) library(msigdbr) library(fgsea) library(ggplot2);library(gridExtra) library(condiments) library(clusterProfiler) epi <- readRDS("fromAvital/Epi_sub_clusters.rds

tradeSeq slingshot

updated 2.4 years ago • manduchi

nbsp;        genefilter\_1.60.0      fgsea\_1.4.0            reshape2\_1.4.2         &nbsp

clusterProfiler

updated 7.1 years ago • GFM

nbsp;     munsell\_0.4.3          fgsea\_1.2.1           \[25\] compiler\_3.4.0         KEGGREST

pathview

updated 7.6 years ago • joseph

nbsp;        \[21\] RColorBrewer\_1.1-2          fgsea\_1.6.0                 Rcpp\_0.12.18                forcats\_0.3.0

deseq2 phyloseq

updated 6.3 years ago • eoin

_1.46.2           loaded via a namespace (and not attached):   \[1\] fgsea\_1.6.0           colorspace\_1.3-2      ggridges\_0.5.0        rprojroot\_1.3

flowworkspace parseWorkspace parseWorkspace

updated 6.3 years ago • vonskopnik

2021-01-25 [1] CRAN (R 4.2.0) fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.2.0) fgsea * 1.22.0 2022-04-26 [1] Bioconductor filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0) fitdistrplus 1.1-8 2022-03-10 [1] CRAN (R 4.2.0) fs

clusterProfiler

updated 2.4 years ago • Y.K