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GSEA
•
reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 8.4 years ago by
Robert Castelo
★ 3.2k • written 8.4 years ago by
jacorvar
▴ 40
9
votes
6
replies
5.5k
views
GSEA-like enrichment score calculation
GSEA
enrichment analysis
gseabase
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
Matthias Z.
▴ 20
9
votes
13
replies
6.3k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 10 weeks ago by
ATpoint
★ 4.0k • written 2.1 years ago by
nhaus
▴ 30
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 9.4 years ago by
Levi Waldron
★ 1.1k • written 9.4 years ago by
kaushal Raj Chaudhary
▴ 10
8
votes
5
replies
3.4k
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
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 12 months ago by
ATpoint
★ 4.0k • written 7.7 years ago by
EJ
▴ 20
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 15 months ago by
Gordon Smyth
50k • written 16 months ago by
nhaus
▴ 30
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.2k • written 4.0 years ago by
rocanja
▴ 60
5
votes
7
replies
2.5k
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
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 830
4
votes
3
replies
202
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 4 weeks ago by
Georg
• 0
4
votes
1
reply
3.2k
views
GSEA using clusterprofileR
clusterprofiler
gsea
updated 6.5 years ago by
alserg
▴ 240 • written 6.5 years ago by
sup230
▴ 30
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
bmreilly
• 0
3
votes
3
replies
1.5k
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
2
votes
4
replies
3.0k
views
Arguments for camera (gene set analysis)
camera
GSEA
updated 8.1 years ago by
Steve Lianoglou
★ 13k • written 8.1 years ago by
claire.n.levy
▴ 10
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
7.3 years ago • updated 7.2 years ago
Pekka Kohonen
▴ 190
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea
gsea
updated 7.3 years ago by
alserg
▴ 240 • written 7.3 years ago by
rubi
▴ 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 5.1 years ago by
Pietro
▴ 40
2
votes
2
replies
3.0k
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
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.2k • written 3.8 years ago by
igor
▴ 40
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
6.7 years ago
cabezasdelafuented
▴ 10
2
votes
1
reply
964
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
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 6.7 years ago by
Andrew_McDavid
▴ 270 • written 6.7 years ago by
siajunren
• 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
2
votes
4
replies
1.6k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA
DEG
updated 8.1 years ago by
Gordon Smyth
50k • written 8.1 years ago by
Shamim Sarhadi
▴ 20
2
votes
1
reply
176
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
enee
▴ 10
2
votes
3
replies
894
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 17 months ago by
gabriel.odom
• 0 • written 17 months ago by
Mikołaj Mierzejewski
• 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
6.4 years ago
giuseppe0525
• 0
2
votes
3
replies
901
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 15 months ago by
belinda.phipson
▴ 40 • written 15 months ago by
Lukas
• 0
2
votes
2
replies
4.0k
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
5
replies
2.0k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 6.7 years ago by
alserg
▴ 240 • written 6.7 years ago by
shawn.w.foley
• 0
1
vote
1
reply
1.2k
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 7.1 years ago by
Guido Hooiveld
★ 3.9k • written 7.1 years ago by
danielle.newby
• 0
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
8.5 years ago
Hector Corrada Bravo
▴ 60
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
6.3 years ago
Stane
▴ 40
1
vote
2
replies
2.0k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 7.1 years ago by
predeus
• 0 • written 9.1 years ago by
Nemo
▴ 80
1
vote
1
reply
933
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
1
vote
0
replies
1.3k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea
ncrna
coexpression
gene set analysis
gene set testing
8.0 years ago
m.fletcher
▴ 20
1
vote
2
replies
2.3k
views
GSVA for single sample
gsea
gsva
ssgsea
6.2 years ago
jaison75
▴ 20
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 7.4 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
rubi
▴ 110
1
vote
2
replies
894
views
giving weight to DEG from limma output
limma
GSEA
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Shamim Sarhadi
▴ 20
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
1
vote
1
reply
1.1k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray
GSEA
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Sanches
• 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.8 years ago
martin.busch
• 0
0
votes
1
reply
590
views
GSA type of input data
GSEA
GSA
vst
updated 15 months ago by
Michael Love
41k • written 15 months ago by
nhaus
▴ 30
0
votes
1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
6.4 years ago
giuseppe0525
• 0
0
votes
6
replies
2.6k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage
gsea
rnaseq
updated 9.0 years ago by
Luo Weijun
★ 1.6k • written 9.0 years ago by
Tom
• 0
0
votes
0
replies
1.1k
views
GSEA with variant proportions as input
GSEA
Variant Proportions
Input
8.7 years ago
manali.rupji
• 0
0
votes
5
replies
1.6k
views
gene set (enrichment) analysis
gsea
gsa
updated 8.1 years ago by
Axel Klenk
★ 1.0k • written 8.1 years ago by
Bogdan
▴ 670
0
votes
13
replies
2.1k
views
Gage and setp argument
gsea
gage
7.9 years ago
peter.chernek
• 0
0
votes
1
reply
2.4k
views
ClusterProfiler can't load gmt file
GSEA
clusterprofiler
gmt
updated 7.7 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
sarah.blackstone7734
• 0
50 results • Page
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Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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