Showing : GSEa • reset
0
votes
2
replies
320
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
4 weeks ago • updated 21 days ago Gordon • 0
2
votes
1
reply
186
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 4 weeks ago by ▴ 10
4
votes
3
replies
208
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 5 weeks ago by • 0
0
votes
1
reply
564
views
choosing rank for GSEA
gsea DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
0
votes
3
replies
1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 6 months ago by • 0 • written 8 months ago by • 0
0
votes
0
replies
595
views
using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 0
1
vote
1
reply
951
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
votes
3
replies
908
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
0
votes
1
reply
591
views
GSA type of input data
GSEA GSA vst
updated 15 months ago by 41k • written 16 months ago by ▴ 30
0
votes
1
reply
794
views
DGE genes are not available in GSEA
dge gsea
updated 16 months ago by ★ 3.9k • written 16 months ago by • 0
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 16 months ago by ▴ 30
2
votes
3
replies
899
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 17 months ago by • 0 • written 17 months ago by • 0
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 21 months ago by 50k • written 21 months ago by ▴ 10
0
votes
3
replies
1.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 17 months ago by ▴ 60 • written 21 months ago by • 0
0
votes
2
replies
3.2k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
22 months ago Bhavana • 0
0
votes
1
reply
1.0k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by ▴ 10
9
votes
13
replies
6.4k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
2
votes
1
reply
967
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
2
replies
2.2k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.2 years ago Emilia ▴ 30
0
votes
1
reply
797
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.4 years ago lessismore ▴ 20
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 60
2
votes
2
replies
3.0k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
8
votes
5
replies
3.4k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 110
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.3 years ago by • 0 • written 5.1 years ago by ▴ 40
0
votes
1
reply
801
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.1 years ago Diana ▴ 10
0
votes
1
reply
2.4k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.1 years ago aboumarshal • 0
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
3
votes
3
replies
1.5k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 50
0
votes
3
replies
1.3k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.3 years ago by 0 • written 5.4 years ago by • 0
0
votes
2
replies
1.3k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 5.5 years ago by ▴ 50 • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
2
replies
1.6k
views
gene set enrichment analysis
GSEA GSA
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 670
0
votes
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.6 years ago santos22903 • 0
5
votes
7
replies
2.5k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.7 years ago l.brown ▴ 10
0
votes
3
replies
2.8k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.8 years ago atakanekiz ▴ 30
0
votes
3
replies
1.7k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
1
vote
1
reply
1.4k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 20
2
votes
2
replies
4.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
0
votes
2
replies
1.6k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 years ago Stane ▴ 40
0
votes
0
replies
1.2k
views
GSEA-class file (.cls) parsing error message
gsea
6.3 years ago snguyen268 • 0
0
votes
1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.4 years ago giuseppe0525 • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago • updated 6.4 years ago giuseppe0525 • 0
4
votes
1
reply
3.2k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.5 years ago by ▴ 240 • written 6.5 years ago by ▴ 30
0
votes
1
reply
1.1k
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
6.6 years ago Seymoo • 0
0
votes
2
replies
1.6k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA GO goSlim
6.6 years ago maeva.mollion • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Awards • All
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
Popular Question to i.sudbery ▴ 40
Scholar to Michael Love 41k
Popular Question to shepherl 3.8k
Locations • All
The Netherlands, just now
Wageningen University, Wageningen, the Netherlands, just now
France, 8 minutes ago
South Korea, 15 minutes ago
France, 16 minutes ago
Traffic: 844 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6