Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
GSEA
•
reset
2
votes
4
replies
210
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 18 days ago by
Gordon Smyth
46k • written 20 days ago by
Yang Shi
• 0
0
votes
2
replies
187
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
5 weeks ago • updated 26 days ago
João
• 0
0
votes
2
replies
132
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
6 weeks ago
Bhavana
• 0
0
votes
1
reply
199
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 4 months ago by
Robert Castelo
★ 2.9k • written 4 months ago by
jms2520
• 0
7
votes
11
replies
863
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 4 months ago by
Gordon Smyth
46k • written 4 months ago by
nhaus
• 0
2
votes
1
reply
367
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 16 months ago by
Kevin Blighe
3.6k • written 16 months ago by
MOHAMMAD
• 0
0
votes
2
replies
977
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
18 months ago
Emilia
▴ 30
0
votes
1
reply
323
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
20 months ago
lessismore
▴ 20
2
votes
1
reply
731
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 2.1 years ago by
Robert Castelo
★ 2.9k • written 2.1 years ago by
igor
▴ 40
7
votes
11
replies
996
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 2.3 years ago by
Robert Castelo
★ 2.9k • written 2.3 years ago by
rocanja
▴ 60
0
votes
2
replies
1.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 3.1 years ago by
Ludwig Geistlinger
▴ 50 • written 3.1 years ago by
lucap
• 0
8
votes
5
replies
1.7k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 3.3 years ago by
Gordon Smyth
46k • written 3.3 years ago by
Biologist
▴ 90
2
votes
4
replies
1.2k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 19 months ago by
bhuva.d
• 0 • written 3.4 years ago by
Pietro
▴ 30
0
votes
1
reply
408
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
3.4 years ago
Diana
▴ 10
0
votes
1
reply
788
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
3.4 years ago
aboumarshal
• 0
3
votes
7
replies
16k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
bmreilly
• 0
3
votes
3
replies
699
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 3.5 years ago by
Peter Langfelder
★ 2.7k • written 3.5 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
759
views
gseaplot vertical line
clusterProfiler
gsea
updated 3.6 years ago by
Bioconductor Community
0 • written 3.7 years ago by
abelsousa
• 0
0
votes
2
replies
665
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 3.8 years ago by
lhuang7
▴ 50 • written 3.8 years ago by
thkapell
▴ 10
0
votes
1
reply
671
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 3.8 years ago by
Michael Love
37k • written 3.8 years ago by
leo_CD
• 0
0
votes
2
replies
837
views
gene set enrichment analysis
GSEA
GSA
updated 3.8 years ago by
Gordon Smyth
46k • written 3.8 years ago by
Bogdan
▴ 640
0
votes
2
replies
629
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
3.9 years ago
santos22903
• 0
5
votes
7
replies
1.1k
views
GSEA for RNA-seq analysis
GSEA
Limma
preranked GSEA
tTest
updated 4.0 years ago by
Gordon Smyth
46k • written 4.0 years ago by
imalumberjack
▴ 10
0
votes
0
replies
591
views
Job:
2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job
rna-seq
chipseq
gsea
python
Job
4.0 years ago
l.brown
▴ 10
0
votes
3
replies
1.3k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
4.1 years ago
atakanekiz
▴ 30
0
votes
3
replies
1.1k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 4.1 years ago by
Michael Love
37k • written 4.2 years ago by
csijst
• 0
1
vote
2
replies
1.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
4.2 years ago
martin.busch
• 0
1
vote
1
reply
837
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea
rattus norvegicus
updated 4.3 years ago by
Gordon Smyth
46k • written 4.3 years ago by
Aurora
▴ 20
2
votes
2
replies
2.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 4.4 years ago by
Guangchuang Yu
★ 1.2k • written 4.4 years ago by
thomasjenner333
• 0
1
vote
2
replies
1.3k
views
GSVA for single sample
gsea
gsva
ssgsea
4.5 years ago
jaison75
▴ 20
0
votes
2
replies
811
views
merging gseaResult objects
clusterprofiler
gsea
updated 4.5 years ago by
Guangchuang Yu
★ 1.2k • written 4.5 years ago by
robmarin
• 0
1
vote
1
reply
861
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
4.6 years ago
Stane
▴ 40
0
votes
0
replies
753
views
GSEA-class file (.cls) parsing error message
gsea
4.6 years ago
snguyen268
• 0
0
votes
1
reply
1.4k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
4.7 years ago
giuseppe0525
• 0
2
votes
6
replies
6.5k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
4.8 years ago • updated 4.7 years ago
giuseppe0525
• 0
4
votes
1
reply
1.8k
views
GSEA using clusterprofileR
clusterprofiler
gsea
updated 4.8 years ago by
assaron
▴ 200 • written 4.8 years ago by
sup230
▴ 30
0
votes
1
reply
612
views
BioQC R package issue with broad gmt files
R
BioQC
gmt
GSEA
4.8 years ago
Seymoo
• 0
0
votes
2
replies
933
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA
GO
goSlim
4.9 years ago
maeva.mollion
• 0
1
vote
1
reply
712
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray
GSEA
updated 4.9 years ago by
Gordon Smyth
46k • written 4.9 years ago by
Sanches
• 0
2
votes
3
replies
1.3k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
5.0 years ago
cabezasdelafuented
▴ 10
2
votes
1
reply
2.8k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 5.0 years ago by
Andrew_McDavid
▴ 260 • written 5.0 years ago by
siajunren
• 0
1
vote
5
replies
1.3k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 5.0 years ago by
assaron
▴ 200 • written 5.0 years ago by
shawn.w.foley
• 0
0
votes
1
reply
845
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
5.2 years ago
bhgyu
▴ 30
0
votes
1
reply
1.3k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 5.3 years ago by
Luo Weijun
★ 1.5k • written 5.3 years ago by
snishtala03
• 0
1
vote
1
reply
770
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA
PAGE
microarray
differential gene expression
pathway analysis
updated 5.4 years ago by
Guido Hooiveld
★ 3.3k • written 5.4 years ago by
danielle.newby
• 0
0
votes
3
replies
1.4k
views
topGO - treating up- and down-regulated genes separately
topGO
GSEA
pathway analysis
updated 5.4 years ago by
Lluís Revilla Sancho
▴ 690 • written 5.4 years ago by
predeus
• 0
1
vote
2
replies
1.5k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 5.4 years ago by
predeus
• 0 • written 7.4 years ago by
Nemo
▴ 80
2
votes
3
replies
1.0k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
5.6 years ago • updated 5.5 years ago
Pekka Kohonen
▴ 190
0
votes
7
replies
1.3k
views
Statistic for GSA
gsea
concept
gsa
updated 5.5 years ago by
Pekka Kohonen
▴ 190 • written 5.5 years ago by
Lluís Revilla Sancho
▴ 690
2
votes
1
reply
968
views
Direction aware fgsea test
fgsea
gsea
updated 5.6 years ago by
assaron
▴ 200 • written 5.6 years ago by
rubi
▴ 100
50 results • Page
1 of 1
Recent ...
Replies
Comment: OPLS-DA: confidence interval for accuracy metric
by
etienne.thevenot
▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
Awards
• All
Popular Question
to
Alejandro Reyes
★ 1.8k
Popular Question
to
Leonardo Collado Torres
▴ 1000
Scholar
to
ATpoint
★ 1.4k
Scholar
to
voogd.o
▴ 10
Popular Question
to
Bumble
▴ 10
Locations
• All
Germany,
just now
WEHI, Melbourne, Australia,
4 minutes ago
Belgium,
8 minutes ago
Netherlands,
10 minutes ago
Zheng Zhou,
15 minutes ago
Traffic: 420 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6