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GSEA
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reset
9
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13
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6.4k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.0k • written 2.1 years ago by
nhaus
▴ 30
0
votes
2
replies
334
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 25 days ago
Gordon
• 0
1
vote
1
reply
964
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
manuelsokolov
• 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
Fatemeh
• 0 • written 8 months ago by
Cen
• 0
0
votes
1
reply
574
views
choosing rank for GSEA
gsea
DESeq2
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Grace.Ciabattoni
• 0
4
votes
3
replies
216
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 5 weeks ago by
Georg
• 0
2
votes
1
reply
196
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
605
views
using fgsea to compare two datasets
GSEA
fgsea
9 months ago
Cen
• 0
8 results • Page
1 of 1
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
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)
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Leo Lahti
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James W. MacDonald
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