Showing : GSEA • reset
0
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331
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
5 weeks ago • updated 23 days ago Gordon • 0
2
votes
1
reply
194
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 5 weeks ago by ▴ 10
4
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3
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211
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 5 weeks ago by • 0
0
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1
reply
572
views
choosing rank for GSEA
gsea DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
0
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3
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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
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0
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599
views
using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 0
1
vote
1
reply
962
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 0
7
votes
8
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11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
2
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3
replies
916
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
0
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1
reply
595
views
GSA type of input data
GSEA GSA vst
updated 16 months ago by 41k • written 16 months ago by ▴ 30
0
votes
1
reply
801
views
DGE genes are not available in GSEA
dge gsea
updated 16 months ago by ★ 3.9k • written 16 months ago by • 0
7
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6
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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
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3
replies
905
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 months ago by • 0
2
votes
4
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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
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1.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 18 months ago by ▴ 60 • written 22 months ago by • 0
0
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2
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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
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1
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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
971
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
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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
801
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.4 years ago lessismore ▴ 20
2
votes
1
reply
2.1k
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
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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
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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
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1
reply
805
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.1 years ago Diana ▴ 10
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1
reply
2.4k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.1 years ago aboumarshal • 0
3
votes
7
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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
1.6k
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
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3
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1.3k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.3 years ago by 0 • written 5.5 years ago by • 0
0
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2
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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
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1
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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
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2
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1.6k
views
gene set enrichment analysis
GSEA GSA
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 670
0
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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
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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
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0
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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
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3
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2.8k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.8 years ago atakanekiz ▴ 30
0
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3
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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
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2
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1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
1
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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
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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
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2
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2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
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2
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1.6k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
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1
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1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 years ago Stane ▴ 40
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0
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1.2k
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GSEA-class file (.cls) parsing error message
gsea
6.3 years ago snguyen268 • 0
0
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1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.4 years ago giuseppe0525 • 0
2
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6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago • updated 6.4 years ago giuseppe0525 • 0
4
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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
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1
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1.1k
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
6.6 years ago Seymoo • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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