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GSEa
•
reset
0
votes
0
replies
1.8k
views
GSEA-class file (.cls) parsing error message
gsea
8.0 years ago
snguyen268
• 0
0
votes
1
reply
3.6k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
8.1 years ago
giuseppe0525
• 0
2
votes
6
replies
16k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
8.1 years ago
giuseppe0525
• 0
4
votes
2
replies
6.2k
views
GSEA using clusterprofileR
clusterprofiler
gsea
written 8.2 years ago by
sup230
▴ 30
0
votes
1
reply
1.6k
views
BioQC R package issue with broad gmt files
R
BioQC
gmt
GSEA
8.2 years ago
Seymoo
• 0
0
votes
2
replies
2.2k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA
GO
goSlim
8.3 years ago
maeva.mollion
• 0
1
vote
1
reply
1.4k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray
GSEA
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
Sanches
• 0
2
votes
3
replies
2.3k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
8.4 years ago
cabezasdelafuented
▴ 10
2
votes
1
reply
5.4k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 8.4 years ago by
Andrew_McDavid
▴ 280 • written 8.4 years ago by
siajunren
• 0
1
vote
5
replies
2.9k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 8.4 years ago by
alserg
▴ 280 • written 8.4 years ago by
shawn.w.foley
• 0
0
votes
1
reply
1.8k
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
8.5 years ago
bhgyu
▴ 30
0
votes
1
reply
2.5k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 8.6 years ago by
Luo Weijun
★ 1.6k • written 8.6 years ago by
snishtala03
• 0
1
vote
1
reply
1.6k
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 8.8 years ago by
Guido Hooiveld
★ 4.1k • written 8.8 years ago by
danielle.newby
• 0
0
votes
3
replies
3.2k
views
topGO - treating up- and down-regulated genes separately
topGO
GSEA
pathway analysis
updated 8.8 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.8 years ago by
predeus
• 0
1
vote
2
replies
2.5k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 8.8 years ago by
predeus
• 0 • written 10.8 years ago by
Nemo
▴ 80
2
votes
4
replies
2.5k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 19 months ago by
Chris
▴ 20 • written 9.0 years ago by
Pekka Kohonen
▴ 190
0
votes
7
replies
3.1k
views
Statistic for GSA
gsea
concept
gsa
updated 8.9 years ago by
Pekka Kohonen
▴ 190 • written 8.9 years ago by
Lluís Revilla Sancho
▴ 760
2
votes
1
reply
2.3k
views
Direction aware fgsea test
fgsea
gsea
updated 8.9 years ago by
alserg
▴ 280 • written 8.9 years ago by
rubi
▴ 110
1
vote
4
replies
3.1k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 9.1 years ago by
Guangchuang Yu
★ 1.2k • written 9.3 years ago by
rubi
▴ 110
0
votes
4
replies
2.6k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 9.3 years ago by
Monther Alhamdoosh
▴ 40 • written 9.3 years ago by
yingchen
• 0
0
votes
1
reply
3.4k
views
ClusterProfiler can't load gmt file
GSEA
clusterprofiler
gmt
updated 9.4 years ago by
Guangchuang Yu
★ 1.2k • written 9.4 years ago by
sarah.blackstone7734
• 0
9
votes
6
replies
7.2k
views
GSEA-like enrichment score calculation
GSEA
enrichment analysis
gseabase
updated 9.5 years ago by
Gordon Smyth
53k • written 9.5 years ago by
Matthias Z.
▴ 20
0
votes
13
replies
3.1k
views
Gage and setp argument
gsea
gage
9.6 years ago
peter.chernek
• 0
1
vote
0
replies
1.9k
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
9.7 years ago
m.fletcher
▴ 20
0
votes
5
replies
2.2k
views
gene set (enrichment) analysis
gsea
gsa
updated 9.8 years ago by
Axel Klenk
★ 1.1k • written 9.8 years ago by
Bogdan
▴ 670
2
votes
4
replies
2.2k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA
DEG
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
Shamim Sarhadi
▴ 20
1
vote
2
replies
1.2k
views
giving weight to DEG from limma output
limma
GSEA
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
3.8k
views
Arguments for camera (gene set analysis)
camera
GSEA
updated 9.8 years ago by
Steve Lianoglou
★ 13k • written 9.8 years ago by
claire.n.levy
▴ 10
13
votes
2
replies
5.5k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 10.1 years ago by
Robert Castelo
★ 3.4k • written 10.1 years ago by
jacorvar
▴ 40
1
vote
0
replies
1.8k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
10.2 years ago
Hector Corrada Bravo
▴ 60
0
votes
0
replies
1.4k
views
GSEA with variant proportions as input
GSEA
Variant Proportions
Input
10.4 years ago
manali.rupji
• 0
5
votes
11
replies
2.5k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 10.5 years ago by
Aaron Lun
★ 29k • written 10.5 years ago by
svlachavas
▴ 840
0
votes
6
replies
3.5k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage
gsea
rnaseq
updated 10.7 years ago by
Luo Weijun
★ 1.6k • written 10.7 years ago by
Tom
• 0
8
votes
16
replies
7.6k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 11.1 years ago by
Levi Waldron
★ 1.1k • written 11.1 years ago by
kaushal Raj Chaudhary
▴ 10
84 results • Page
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Comment: Limma-voom sample weights and impact on DEG numbers
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I have faced similar issues before, and often the problem comes down to package versions or R/Bioconductor compatibility. Make sure your R …
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Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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Gordon Smyth
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Istvan Albert
▴ 50
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★ 1.6k
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