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GSEa
•
reset
9
votes
13
replies
6.7k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 2.2 years ago by
nhaus
▴ 30
4
votes
3
replies
241
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 8 weeks ago by
Georg
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 4 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
2
votes
1
reply
221
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 3.9k • written 7 weeks ago by
enee
▴ 10
1
vote
1
reply
1.0k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
0
votes
0
replies
631
views
using fgsea to compare two datasets
GSEA
fgsea
9 months ago
Cen
• 0
0
votes
1
reply
631
views
choosing rank for GSEA
gsea
DESeq2
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
Grace.Ciabattoni
• 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 9 months ago by
Cen
• 0
0
votes
2
replies
365
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
7 weeks ago • updated 5 weeks ago
Gordon
• 0
9 results • Page
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Comment: Problem finding certain variables when importing a public database GSE73103
by
Guido Hooiveld
★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue
by
shepherl
3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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ATpoint
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