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GSEA
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9
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13
replies
6.8k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.2k • written 2.2 years ago by
nhaus
▴ 40
4
votes
3
replies
275
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 9 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 17 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
2
votes
1
reply
248
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 9 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
654
views
using fgsea to compare two datasets
GSEA
fgsea
10 months ago
Cen
• 0
0
votes
1
reply
692
views
choosing rank for GSEA
gsea
DESeq2
updated 7 months ago by
ATpoint
★ 4.2k • written 7 months ago by
Grace.Ciabattoni
• 0
0
votes
3
replies
1.4k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 7 months ago by
Fatemeh
• 0 • written 9 months ago by
Cen
• 0
0
votes
2
replies
386
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
9 weeks ago • updated 7 weeks ago
Gordon
• 0
9 results • Page
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Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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