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Showing :
genesetenrichment
•
reset
2
votes
2
replies
678
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
3 months ago • updated 12 weeks ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
484
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 4 months ago by
ATpoint
★ 4.6k • written 4 months ago by
picasa1983
• 0
0
votes
1
reply
705
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 6 months ago by
Guido Hooiveld
★ 4.1k • written 6 months ago by
aogunbaw
• 0
1
vote
2
replies
1.1k
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
7 months ago
Ana
• 0
0
votes
2
replies
556
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
8 months ago
Seongsu
• 0
4
votes
4
replies
4.3k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 8 months ago by
jandrade
• 0 • written 7.0 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
0
replies
554
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
16 months ago
sonal
• 0
0
votes
1
reply
1.4k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 16 months ago by
James W. MacDonald
67k • written 16 months ago by
manuelsokolov
• 0
0
votes
2
replies
4.7k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.4 years ago
Bhavana
• 0
0
votes
1
reply
1.2k
views
enrichment to common gene
GeneSetEnrichment
genes
genetogo
updated 2.5 years ago by
Basti
▴ 780 • written 2.5 years ago by
Noy
• 0
12
votes
13
replies
9.4k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 10 months ago by
ATpoint
★ 4.6k • written 2.7 years ago by
nhaus
▴ 70
1
vote
0
replies
1.6k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
3.1 years ago
makrez
▴ 10
3
votes
2
replies
1.5k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 4.0 years ago by
Gordon Smyth
52k • written 4.0 years ago by
prabin.dm
• 0
0
votes
1
reply
1.6k
views
Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler
GeneSetEnrichment
enrichplot
updated 3.9 years ago by
Emilia
▴ 40 • written 4.0 years ago by
saw44
• 0
0
votes
0
replies
702
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
4.0 years ago
paun_bio
• 0
1
vote
4
replies
3.3k
views
Problem retrieving graphics in clusterprofiler
software error
clusterprofiler
GO
genesetenrichment
8.6 years ago
José Luis Lavín
▴ 10
1
vote
0
replies
1.2k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma
genesetenrichment
updated 8.7 years ago by
Steve Lianoglou
★ 13k • written 8.7 years ago by
Aditya
▴ 160
1
vote
0
replies
1.5k
views
News:
Announcing the EnrichmentBrowser 2.0
genesetenrichment
functional enrichment
enrichmentbrowser
News
8.8 years ago
Ludwig Geistlinger
▴ 70
5
votes
7
replies
5.4k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 9.0 years ago by
Gordon Smyth
52k • written 9.0 years ago by
Jon Bråte
▴ 260
2
votes
1
reply
1.2k
views
elim method for KEGG pathways?
KEGG
genesetenrichment
elim
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
jacorvar
▴ 40
2
votes
2
replies
2.2k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 9.3 years ago by
Nadia Davidson
▴ 320 • written 9.3 years ago by
xyliu00
▴ 20
8
votes
14
replies
4.3k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.7 years ago by
willem.ligtenberg
▴ 150 • written 10.0 years ago by
Guangchuang Yu
★ 1.2k
1
vote
1
reply
5.6k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 9.9 years ago by
Luo Weijun
★ 1.6k • written 9.9 years ago by
Alan Smith
▴ 150
0
votes
0
replies
1.2k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
10.0 years ago
Peter.Wood
• 0
0
votes
0
replies
1.8k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
10.0 years ago
Guangchuang Yu
★ 1.2k
0
votes
3
replies
2.0k
views
Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 10.7 years ago by
Steve Lianoglou
★ 13k • written 10.7 years ago by
Leif Väremo
▴ 70
26 results • Page
1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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