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Showing :
gsea
•
reset
0
votes
4
replies
673
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
3 months ago
Quang NN
▴ 10
1
vote
8
replies
1.2k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea
mice
org.Mm.eg.db
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
Gordon
• 0
1
vote
2
replies
2.4k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 7 months ago by
b8177
• 0
0
votes
1
reply
816
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 8 months ago by
Axel Klenk
★ 1.1k • written 8 months ago by
Bioinformagician
• 0
1
vote
4
replies
1.2k
views
Error in gseDO function
DOSE
gsea
11 months ago
Javier
• 0
0
votes
2
replies
1.5k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
13 months ago
Gordon
• 0
2
votes
2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 13 months ago by
enee
▴ 10
4
votes
3
replies
955
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 13 months ago by
Georg
• 0
0
votes
1
reply
2.0k
views
choosing rank for GSEA
gsea
DESeq2
updated 18 months ago by
ATpoint
★ 4.8k • written 18 months ago by
Grace.Ciabattoni
• 0
0
votes
3
replies
2.8k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 18 months ago by
Fatemeh
• 0 • written 20 months ago by
Cen
• 0
0
votes
0
replies
1.1k
views
using fgsea to compare two datasets
GSEA
fgsea
21 months ago
Cen
• 0
1
vote
1
reply
1.9k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
52k • written 21 months ago by
manuelsokolov
• 0
8
votes
10
replies
16k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 1 day ago by
ATpoint
★ 4.8k • written 8.7 years ago by
EJ
▴ 20
2
votes
3
replies
1.8k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.3 years ago by
belinda.phipson
▴ 40 • written 2.3 years ago by
Lukas
• 0
0
votes
1
reply
877
views
GSA type of input data
GSEA
GSA
vst
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
nhaus
▴ 70
0
votes
1
reply
1.5k
views
DGE genes are not available in GSEA
dge
gsea
updated 2.4 years ago by
Guido Hooiveld
★ 4.1k • written 2.4 years ago by
Lawrence
• 0
7
votes
6
replies
4.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.3 years ago by
Gordon Smyth
52k • written 2.4 years ago by
nhaus
▴ 70
2
votes
3
replies
1.4k
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 2.5 years ago by
gabriel.odom
• 0 • written 2.5 years ago by
Mikołaj Mierzejewski
• 0
2
votes
4
replies
1.8k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 2.8 years ago by
Gordon Smyth
52k • written 2.8 years ago by
Yang Shi
▴ 10
0
votes
3
replies
3.4k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 2.5 years ago by
rocanja
▴ 60 • written 2.8 years ago by
João
• 0
0
votes
2
replies
5.6k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.8 years ago
Bhavana
• 0
0
votes
1
reply
2.1k
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 3.1 years ago by
Robert Castelo
★ 3.4k • written 3.1 years ago by
jms2520
▴ 10
12
votes
13
replies
12k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 14 months ago by
ATpoint
★ 4.8k • written 3.1 years ago by
nhaus
▴ 70
2
votes
1
reply
1.3k
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
MOHAMMAD
• 0
0
votes
2
replies
3.9k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
4.2 years ago
Emilia
▴ 40
0
votes
1
reply
1.1k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
4.4 years ago
lessismore
▴ 20
2
votes
1
reply
3.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.8 years ago by
Robert Castelo
★ 3.4k • written 4.8 years ago by
igor
▴ 50
7
votes
11
replies
3.6k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 5.0 years ago by
Robert Castelo
★ 3.4k • written 5.0 years ago by
rocanja
▴ 60
2
votes
2
replies
4.6k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 5.8 years ago by
Ludwig Geistlinger
▴ 70 • written 5.8 years ago by
lucap
• 0
8
votes
5
replies
4.6k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
Biologist
▴ 120
2
votes
4
replies
3.3k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 4.3 years ago by
Dharmesh D Bhuva
• 0 • written 6.1 years ago by
Pietro
▴ 40
0
votes
1
reply
1.1k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
6.1 years ago
Diana
▴ 10
0
votes
1
reply
3.7k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
6.1 years ago
aboumarshal
• 0
3
votes
7
replies
30k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
bmreilly
• 0
3
votes
3
replies
2.5k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
hamza_karakurt
▴ 60
0
votes
3
replies
1.6k
views
gseaplot vertical line
clusterProfiler
gsea
updated 6.3 years ago by
Bioconductor Community
0 • written 6.5 years ago by
abelsousa
• 0
0
votes
2
replies
1.9k
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 6.5 years ago by
lhuang7
▴ 50 • written 6.5 years ago by
thkapell
▴ 10
0
votes
1
reply
1.5k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
leo_CD
• 0
0
votes
2
replies
2.2k
views
gene set enrichment analysis
GSEA
GSA
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.6k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
6.6 years ago
santos22903
• 0
5
votes
7
replies
3.9k
views
GSEA for RNA-seq analysis
GSEA
Limma
preranked GSEA
tTest
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
imalumberjack
▴ 10
0
votes
0
replies
1.3k
views
Job:
2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job
rna-seq
chipseq
gsea
python
Job
6.7 years ago
l.brown
▴ 10
0
votes
3
replies
4.0k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
6.8 years ago
atakanekiz
▴ 30
0
votes
3
replies
2.2k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
csijst
• 0
1
vote
2
replies
2.2k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.9 years ago
martin.busch
• 0
1
vote
1
reply
1.8k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea
rattus norvegicus
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
Aurora
▴ 20
2
votes
2
replies
5.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
thomasjenner333
• 0
1
vote
2
replies
3.0k
views
GSVA for single sample
gsea
gsva
ssgsea
7.2 years ago
jaison75
▴ 20
0
votes
2
replies
2.2k
views
merging gseaResult objects
clusterprofiler
gsea
updated 7.2 years ago by
Guangchuang Yu
★ 1.2k • written 7.2 years ago by
robmarin
• 0
1
vote
1
reply
2.4k
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
7.3 years ago
Stane
▴ 40
50 results • Page
1 of 1
Recent ...
Replies
Comment: Module membership vs gene significance result and Modules-trait relationships re
by
Vinaya
• 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts
by
Tom
• 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule
by
randyprice13102000
• 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq
by
ATpoint
★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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