Showing : gsea • reset
0
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4
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579
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 weeks ago Quang NN ▴ 10
1
vote
8
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1.2k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
2
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2.2k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 7 months ago by • 0
0
votes
1
reply
739
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 7 months ago by ★ 1.1k • written 7 months ago by • 0
1
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4
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1.1k
views
Error in gseDO function
DOSE gsea
10 months ago Javier • 0
0
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2
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1.4k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
12 months ago Gordon • 0
2
votes
2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 12 months ago by ▴ 10
4
votes
3
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903
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 12 months ago by • 0
0
votes
1
reply
1.9k
views
choosing rank for GSEA
gsea DESeq2
updated 17 months ago by ★ 4.8k • written 17 months ago by • 0
0
votes
3
replies
2.6k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 17 months ago by • 0 • written 20 months ago by • 0
0
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0
replies
1.0k
views
using fgsea to compare two datasets
GSEA fgsea
20 months ago Cen • 0
1
vote
1
reply
1.8k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 21 months ago by 52k • written 21 months ago by • 0
8
votes
8
replies
15k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 23 months ago by ★ 4.8k • written 8.7 years ago by ▴ 20
2
votes
3
replies
1.7k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.2 years ago by ▴ 40 • written 2.2 years ago by • 0
0
votes
1
reply
866
views
GSA type of input data
GSEA GSA vst
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 70
0
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1
reply
1.4k
views
DGE genes are not available in GSEA
dge gsea
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
7
votes
6
replies
4.0k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.3 years ago by 52k • written 2.3 years ago by ▴ 70
2
votes
3
replies
1.4k
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
2
votes
4
replies
1.8k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.7 years ago by 52k • written 2.7 years ago by ▴ 10
0
votes
3
replies
3.2k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.4 years ago by ▴ 60 • written 2.8 years ago by • 0
0
votes
2
replies
5.5k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.8 years ago Bhavana • 0
0
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1
reply
2.0k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 3.0 years ago by ★ 3.4k • written 3.0 years ago by ▴ 10
12
votes
13
replies
11k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 14 months ago by ★ 4.8k • written 3.1 years ago by ▴ 70
2
votes
1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
0
votes
2
replies
3.7k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
4.2 years ago Emilia ▴ 40
0
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1
reply
1.1k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.3 years ago lessismore ▴ 20
2
votes
1
reply
3.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 50
7
votes
11
replies
3.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.9 years ago by ★ 3.4k • written 4.9 years ago by ▴ 60
2
votes
2
replies
4.5k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.7 years ago by ▴ 70 • written 5.8 years ago by • 0
8
votes
5
replies
4.6k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 120
2
votes
4
replies
3.3k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.2 years ago by • 0 • written 6.1 years ago by ▴ 40
0
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1
reply
1.1k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
6.1 years ago Diana ▴ 10
0
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1
reply
3.6k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
6.1 years ago aboumarshal • 0
3
votes
7
replies
29k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
3
votes
3
replies
2.4k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 60
0
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3
replies
1.6k
views
gseaplot vertical line
clusterProfiler gsea
updated 6.2 years ago by 0 • written 6.4 years ago by • 0
0
votes
2
replies
1.9k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 10
0
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1
reply
1.5k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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2
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2.1k
views
gene set enrichment analysis
GSEA GSA
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 670
0
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2
replies
1.6k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.6 years ago santos22903 • 0
5
votes
7
replies
3.8k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.6 years ago by 52k • written 6.7 years ago by ▴ 10
0
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0
replies
1.3k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.7 years ago l.brown ▴ 10
0
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3
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3.9k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.7 years ago atakanekiz ▴ 30
0
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3
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2.2k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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2
replies
2.2k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.8 years ago martin.busch • 0
1
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1
reply
1.7k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 20
2
votes
2
replies
5.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 7.0 years ago by ★ 1.2k • written 7.1 years ago by • 0
1
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2
replies
2.9k
views
GSVA for single sample
gsea gsva ssgsea
7.2 years ago jaison75 ▴ 20
0
votes
2
replies
2.2k
views
merging gseaResult objects
clusterprofiler gsea
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
1
vote
1
reply
2.4k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
7.2 years ago Stane ▴ 40
50 results • Page 1 of 1
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Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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