Showing : GSEA • reset
0
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648
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Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 12 days ago by 67k • written 14 days ago by • 0
1
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2
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734
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 8 weeks ago by • 0
0
votes
1
reply
409
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 12 weeks ago by ★ 1.0k • written 12 weeks ago by • 0
1
vote
4
replies
650
views
Error in gseDO function
DOSE gsea
5 months ago Javier • 0
0
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2
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865
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
7 months ago Gordon • 0
2
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2
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688
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 7 months ago by ▴ 10
4
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3
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609
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 7 months ago by • 0
0
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1
reply
1.3k
views
choosing rank for GSEA
gsea DESeq2
updated 12 months ago by ★ 4.5k • written 12 months ago by • 0
0
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3
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2.0k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 12 months ago by • 0 • written 15 months ago by • 0
0
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0
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864
views
using fgsea to compare two datasets
GSEA fgsea
15 months ago Cen • 0
1
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1
reply
1.4k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 16 months ago by 51k • written 16 months ago by • 0
8
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8
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13k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 18 months ago by ★ 4.5k • written 8.3 years ago by ▴ 20
2
votes
3
replies
1.4k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
0
votes
1
reply
747
views
GSA type of input data
GSEA GSA vst
updated 22 months ago by 42k • written 22 months ago by ▴ 70
0
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1
reply
1.1k
views
DGE genes are not available in GSEA
dge gsea
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
7
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6
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2.9k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 22 months ago by 51k • written 23 months ago by ▴ 70
2
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3
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1.2k
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 2.0 years ago by • 0 • written 2.0 years ago by • 0
2
votes
4
replies
1.6k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.3 years ago by 51k • written 2.3 years ago by ▴ 10
0
votes
3
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2.6k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.0 years ago by ▴ 60 • written 2.3 years ago by • 0
0
votes
2
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4.6k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.4 years ago Bhavana • 0
0
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1
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1.6k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.6 years ago by ★ 3.4k • written 2.6 years ago by ▴ 10
12
votes
13
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9.0k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 9 months ago by ★ 4.5k • written 2.6 years ago by ▴ 70
2
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1
reply
1.1k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
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2
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3.0k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.8 years ago Emilia ▴ 40
0
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1
reply
978
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.9 years ago lessismore ▴ 20
2
votes
1
reply
2.5k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ▴ 50
7
votes
11
replies
3.0k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by ▴ 60
2
votes
2
replies
3.9k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by • 0
8
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5
replies
4.1k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.5 years ago by 51k • written 5.5 years ago by ▴ 120
2
votes
4
replies
2.8k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.8 years ago by • 0 • written 5.7 years ago by ▴ 40
0
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1
reply
971
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.7 years ago Diana ▴ 10
0
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1
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3.1k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.7 years ago aboumarshal • 0
3
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7
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28k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
3
votes
3
replies
1.9k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 60
0
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3
replies
1.5k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.8 years ago by 0 • written 6.0 years ago by • 0
0
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2
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1.6k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.0 years ago by ▴ 50 • written 6.0 years ago by ▴ 10
0
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1
reply
1.3k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
0
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2
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1.9k
views
gene set enrichment analysis
GSEA GSA
updated 6.1 years ago by 51k • written 6.1 years ago by ▴ 670
0
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2
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1.4k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.2 years ago santos22903 • 0
5
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7
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3.3k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.2 years ago by 51k • written 6.2 years ago by ▴ 10
0
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0
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1.2k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.2 years ago l.brown ▴ 10
0
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3
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3.4k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.3 years ago atakanekiz ▴ 30
0
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3
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2.0k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
1
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2
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2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.4 years ago martin.busch • 0
1
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1
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1.5k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.5 years ago by 51k • written 6.5 years ago by ▴ 20
2
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2
replies
4.6k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
1
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2
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2.7k
views
GSVA for single sample
gsea gsva ssgsea
6.7 years ago jaison75 ▴ 20
0
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2
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2.0k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
1
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1
reply
2.2k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.8 years ago Stane ▴ 40
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0
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1.5k
views
GSEA-class file (.cls) parsing error message
gsea
6.8 years ago snguyen268 • 0
50 results • Page 1 of 1
Recent ...
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Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Gordon Smyth 51k
`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample.
Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0
Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…
Answer: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k
Given nf-core's pipeline here, you can use rounded counts from `gene_counts_length_scaled.tsv`.
Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k
You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…
Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0
Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…
Votes
Answer: DESeq Input from Salmon + tximport/tximeta
Answer: featureCounts segmentation fault with large chromosomes
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Awards • All
Popular Question to john • 0
Popular Question to Gordon Smyth 51k
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Commentator to Mike Smith ★ 6.6k
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