Showing : gsea • reset
1
vote
4
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318
views
Error in gseDO function
DOSE gsea
4 weeks ago Javier • 0
0
votes
2
replies
469
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
3 months ago • updated 12 weeks ago Gordon • 0
2
votes
1
reply
332
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 3 months ago by ★ 4.0k • written 3 months ago by ▴ 10
4
votes
3
replies
357
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 3 months ago by • 0
0
votes
1
reply
830
views
choosing rank for GSEA
gsea DESeq2
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
0
votes
3
replies
1.5k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 8 months ago by • 0 • written 10 months ago by • 0
0
votes
0
replies
685
views
using fgsea to compare two datasets
GSEA fgsea
11 months ago Cen • 0
1
vote
1
reply
1.1k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 11 months ago by 51k • written 11 months ago by • 0
7
votes
8
replies
12k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 14 months ago by ★ 4.2k • written 7.9 years ago by ▴ 20
2
votes
3
replies
1.1k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 18 months ago by ▴ 40 • written 18 months ago by • 0
0
votes
1
reply
632
views
GSA type of input data
GSEA GSA vst
updated 18 months ago by 42k • written 18 months ago by ▴ 50
0
votes
1
reply
911
views
DGE genes are not available in GSEA
dge gsea
updated 18 months ago by ★ 4.0k • written 18 months ago by • 0
7
votes
6
replies
2.4k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 18 months ago by 51k • written 18 months ago by ▴ 50
2
votes
3
replies
974
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 20 months ago by • 0 • written 20 months ago by • 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 23 months ago by 51k • written 23 months ago by ▴ 10
0
votes
3
replies
2.1k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 20 months ago by ▴ 60 • written 24 months ago by • 0
0
votes
2
replies
3.7k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.0 years ago Bhavana • 0
0
votes
1
reply
1.2k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.3 years ago by ★ 3.3k • written 2.3 years ago by ▴ 10
10
votes
13
replies
7.2k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 4 months ago by ★ 4.2k • written 2.3 years ago by ▴ 50
2
votes
1
reply
1.0k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by • 0
0
votes
2
replies
2.5k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.4 years ago Emilia ▴ 30
0
votes
1
reply
851
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.6 years ago lessismore ▴ 20
2
votes
1
reply
2.2k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 50
7
votes
11
replies
2.6k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.2 years ago by ★ 3.3k • written 4.2 years ago by ▴ 60
2
votes
2
replies
3.4k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.0 years ago by ▴ 70 • written 5.0 years ago by • 0
8
votes
5
replies
3.7k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.2 years ago by 51k • written 5.2 years ago by ▴ 110
2
votes
4
replies
2.6k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.5 years ago by • 0 • written 5.3 years ago by ▴ 40
0
votes
1
reply
854
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.3 years ago Diana ▴ 10
0
votes
1
reply
2.7k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.3 years ago aboumarshal • 0
3
votes
7
replies
27k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
3
votes
3
replies
1.7k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.3 years ago by ★ 3.0k • written 5.3 years ago by ▴ 60
0
votes
3
replies
1.4k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.5 years ago by 0 • written 5.6 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 5.6 years ago by ▴ 50 • written 5.6 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 5.7 years ago by 42k • written 5.7 years ago by • 0
0
votes
2
replies
1.7k
views
gene set enrichment analysis
GSEA GSA
updated 5.7 years ago by 51k • written 5.7 years ago by ▴ 670
0
votes
2
replies
1.3k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.8 years ago santos22903 • 0
5
votes
7
replies
2.8k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.9 years ago by 51k • written 5.9 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.9 years ago l.brown ▴ 10
0
votes
3
replies
3.0k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.9 years ago atakanekiz ▴ 30
0
votes
3
replies
1.8k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.0 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 6.2 years ago by 51k • written 6.2 years ago by ▴ 20
2
votes
2
replies
4.2k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
1
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2
replies
2.5k
views
GSVA for single sample
gsea gsva ssgsea
6.4 years ago jaison75 ▴ 20
0
votes
2
replies
1.8k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by • 0
1
vote
1
reply
1.9k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.5 years ago Stane ▴ 40
0
votes
0
replies
1.3k
views
GSEA-class file (.cls) parsing error message
gsea
6.5 years ago snguyen268 • 0
0
votes
1
reply
2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.6 years ago giuseppe0525 • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.6 years ago giuseppe0525 • 0
4
votes
1
reply
3.4k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.7 years ago by ▴ 260 • written 6.7 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Ranking the GSEA Results by Michael Love 42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR by Gordon Smyth 51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database by Sean Davis 21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
Awards • All
Popular Question to Gordon Smyth 51k
Popular Question to Sean Davis 21k
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Martin Morgan 25k
Popular Question to Wolfgang Huber ★ 13k
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