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gsea
•
reset
0
votes
0
replies
1.7k
views
GSEA-class file (.cls) parsing error message
gsea
7.7 years ago
snguyen268
• 0
0
votes
1
reply
3.4k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
7.8 years ago
giuseppe0525
• 0
2
votes
6
replies
15k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
7.8 years ago
giuseppe0525
• 0
4
votes
2
replies
5.9k
views
GSEA using clusterprofileR
clusterprofiler
gsea
written 7.9 years ago by
sup230
▴ 30
0
votes
1
reply
1.5k
views
BioQC R package issue with broad gmt files
R
BioQC
gmt
GSEA
7.9 years ago
Seymoo
• 0
0
votes
2
replies
2.1k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA
GO
goSlim
8.0 years ago
maeva.mollion
• 0
1
vote
1
reply
1.3k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray
GSEA
updated 8.0 years ago by
Gordon Smyth
52k • written 8.0 years ago by
Sanches
• 0
2
votes
3
replies
2.2k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
8.1 years ago
cabezasdelafuented
▴ 10
2
votes
1
reply
5.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 8.1 years ago by
Andrew_McDavid
▴ 280 • written 8.1 years ago by
siajunren
• 0
1
vote
5
replies
2.8k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 8.1 years ago by
alserg
▴ 280 • written 8.1 years ago by
shawn.w.foley
• 0
0
votes
1
reply
1.7k
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
8.2 years ago
bhgyu
▴ 30
0
votes
1
reply
2.4k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 8.3 years ago by
Luo Weijun
★ 1.6k • written 8.3 years ago by
snishtala03
• 0
1
vote
1
reply
1.5k
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 8.5 years ago by
Guido Hooiveld
★ 4.1k • written 8.5 years ago by
danielle.newby
• 0
0
votes
3
replies
3.1k
views
topGO - treating up- and down-regulated genes separately
topGO
GSEA
pathway analysis
updated 8.5 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.5 years ago by
predeus
• 0
1
vote
2
replies
2.4k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 8.5 years ago by
predeus
• 0 • written 10.5 years ago by
Nemo
▴ 80
2
votes
4
replies
2.2k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 16 months ago by
Chris
▴ 20 • written 8.7 years ago by
Pekka Kohonen
▴ 190
0
votes
7
replies
2.9k
views
Statistic for GSA
gsea
concept
gsa
updated 8.6 years ago by
Pekka Kohonen
▴ 190 • written 8.6 years ago by
Lluís Revilla Sancho
▴ 760
2
votes
1
reply
2.1k
views
Direction aware fgsea test
fgsea
gsea
updated 8.6 years ago by
alserg
▴ 280 • written 8.6 years ago by
rubi
▴ 110
1
vote
4
replies
3.0k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 8.8 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
rubi
▴ 110
0
votes
4
replies
2.5k
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 8.9 years ago by
Monther Alhamdoosh
▴ 40 • written 8.9 years ago by
yingchen
• 0
0
votes
1
reply
3.2k
views
ClusterProfiler can't load gmt file
GSEA
clusterprofiler
gmt
updated 9.1 years ago by
Guangchuang Yu
★ 1.2k • written 9.1 years ago by
sarah.blackstone7734
• 0
9
votes
6
replies
7.0k
views
GSEA-like enrichment score calculation
GSEA
enrichment analysis
gseabase
updated 9.2 years ago by
Gordon Smyth
52k • written 9.2 years ago by
Matthias Z.
▴ 20
0
votes
13
replies
2.9k
views
Gage and setp argument
gsea
gage
9.3 years ago
peter.chernek
• 0
1
vote
0
replies
1.7k
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
9.4 years ago
m.fletcher
▴ 20
0
votes
5
replies
2.0k
views
gene set (enrichment) analysis
gsea
gsa
updated 9.5 years ago by
Axel Klenk
★ 1.1k • written 9.5 years ago by
Bogdan
▴ 670
2
votes
4
replies
2.1k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA
DEG
updated 9.5 years ago by
Gordon Smyth
52k • written 9.5 years ago by
Shamim Sarhadi
▴ 20
1
vote
2
replies
1.1k
views
giving weight to DEG from limma output
limma
GSEA
updated 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
3.6k
views
Arguments for camera (gene set analysis)
camera
GSEA
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
claire.n.levy
▴ 10
13
votes
2
replies
5.3k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 9.8 years ago by
Robert Castelo
★ 3.4k • written 9.8 years ago by
jacorvar
▴ 40
1
vote
0
replies
1.7k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
9.9 years ago
Hector Corrada Bravo
▴ 60
0
votes
0
replies
1.3k
views
GSEA with variant proportions as input
GSEA
Variant Proportions
Input
10.1 years ago
manali.rupji
• 0
5
votes
11
replies
2.3k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 10.2 years ago by
Aaron Lun
★ 29k • written 10.2 years ago by
svlachavas
▴ 840
0
votes
6
replies
3.4k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage
gsea
rnaseq
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
Tom
• 0
8
votes
16
replies
7.4k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 10.8 years ago by
Levi Waldron
★ 1.1k • written 10.8 years ago by
kaushal Raj Chaudhary
▴ 10
84 results • Page
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Comment: WGCNA analysis on RNAseq and proteoimcs data
by
sum31278
• 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning
by
inadequate.peacock.iiag
• 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design
by
Gordon Smyth
52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design
by
James W. MacDonald
68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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