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GSEa
•
reset
0
votes
2
replies
358
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
6 weeks ago • updated 4 weeks ago
Gordon
• 0
2
votes
1
reply
212
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
4
votes
3
replies
232
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 6 weeks ago by
Georg
• 0
0
votes
1
reply
607
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 8 months ago by
Cen
• 0
0
votes
0
replies
616
views
using fgsea to compare two datasets
GSEA
fgsea
9 months ago
Cen
• 0
1
vote
1
reply
984
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
2
votes
3
replies
941
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 16 months ago by
belinda.phipson
▴ 40 • written 16 months ago by
Lukas
• 0
0
votes
1
reply
600
views
GSA type of input data
GSEA
GSA
vst
updated 16 months ago by
Michael Love
41k • written 16 months ago by
nhaus
▴ 30
0
votes
1
reply
813
views
DGE genes are not available in GSEA
dge
gsea
updated 17 months ago by
Guido Hooiveld
★ 3.9k • written 17 months ago by
Lawrence
• 0
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 16 months ago by
Gordon Smyth
50k • written 17 months ago by
nhaus
▴ 30
2
votes
3
replies
916
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 18 months ago by
gabriel.odom
• 0 • written 18 months ago by
Mikołaj Mierzejewski
• 0
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
0
votes
3
replies
1.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 18 months ago by
rocanja
▴ 60 • written 22 months ago by
João
• 0
0
votes
2
replies
3.3k
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
votes
1
reply
1.1k
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
jms2520
▴ 10
9
votes
13
replies
6.5k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 2.1 years ago by
nhaus
▴ 30
2
votes
1
reply
979
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
0
votes
2
replies
2.3k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
3.3 years ago
Emilia
▴ 30
0
votes
1
reply
814
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
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 40
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
rocanja
▴ 60
2
votes
2
replies
3.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 4.8 years ago by
Ludwig Geistlinger
▴ 70 • written 4.8 years ago by
lucap
• 0
8
votes
5
replies
3.5k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Biologist
▴ 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
Dharmesh D Bhuva
• 0 • written 5.2 years ago by
Pietro
▴ 40
0
votes
1
reply
813
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
5.2 years ago
Diana
▴ 10
0
votes
1
reply
2.5k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.2 years ago
aboumarshal
• 0
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
bmreilly
• 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
Peter Langfelder
★ 3.0k • written 5.2 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
1.3k
views
gseaplot vertical line
clusterProfiler
gsea
updated 5.3 years ago by
Bioconductor Community
0 • written 5.5 years ago by
abelsousa
• 0
0
votes
2
replies
1.3k
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 5.5 years ago by
lhuang7
▴ 50 • written 5.5 years ago by
thkapell
▴ 10
0
votes
1
reply
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
Michael Love
41k • written 5.5 years ago by
leo_CD
• 0
0
votes
2
replies
1.6k
views
gene set enrichment analysis
GSEA
GSA
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
5.7 years ago
santos22903
• 0
5
votes
7
replies
2.6k
views
GSEA for RNA-seq analysis
GSEA
Limma
preranked GSEA
tTest
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
imalumberjack
▴ 10
0
votes
0
replies
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
votes
3
replies
2.8k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
5.8 years ago
atakanekiz
▴ 30
0
votes
3
replies
1.7k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
csijst
• 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.9 years ago
martin.busch
• 0
1
vote
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
Gordon Smyth
50k • written 6.0 years ago by
Aurora
▴ 20
2
votes
2
replies
4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
thomasjenner333
• 0
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea
gsva
ssgsea
6.2 years ago
jaison75
▴ 20
0
votes
2
replies
1.7k
views
merging gseaResult objects
clusterprofiler
gsea
updated 6.3 years ago by
Guangchuang Yu
★ 1.2k • written 6.3 years ago by
robmarin
• 0
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
6.3 years ago
Stane
▴ 40
0
votes
0
replies
1.3k
views
GSEA-class file (.cls) parsing error message
gsea
6.3 years ago
snguyen268
• 0
0
votes
1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
6.5 years ago
giuseppe0525
• 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
6.5 years ago
giuseppe0525
• 0
4
votes
1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler
gsea
updated 6.6 years ago by
alserg
▴ 260 • written 6.6 years ago by
sup230
▴ 30
0
votes
1
reply
1.1k
views
BioQC R package issue with broad gmt files
R
BioQC
gmt
GSEA
6.6 years ago
Seymoo
• 0
0
votes
2
replies
1.6k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA
GO
goSlim
6.6 years ago
maeva.mollion
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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