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GeneSetEnrichment
•
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0
votes
0
replies
218
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
8 weeks ago
GT
• 0
0
votes
0
replies
161
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
11 weeks ago
info
▴ 10
0
votes
2
replies
482
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
12 weeks ago • updated 11 weeks ago
Hugo Varet
▴ 80
0
votes
1
reply
419
views
News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
12 weeks ago • updated 11 weeks ago
info
▴ 10
0
votes
1
reply
221
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Sahil
• 0
2
votes
2
replies
984
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
8 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
981
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 10 months ago by
ATpoint
★ 4.8k • written 10 months ago by
picasa1983
• 0
0
votes
1
reply
1.2k
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 12 months ago by
Guido Hooiveld
★ 4.1k • written 12 months ago by
aogunbaw
• 0
1
vote
2
replies
2.0k
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
13 months ago
Ana
• 0
0
votes
2
replies
847
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
13 months ago
Seongsu
• 0
4
votes
4
replies
4.9k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 14 months ago by
jandrade
• 0 • written 7.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
0
replies
698
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
22 months ago
sonal
• 0
0
votes
1
reply
1.9k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
manuelsokolov
• 0
0
votes
2
replies
5.7k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.9 years ago
Bhavana
• 0
0
votes
1
reply
1.5k
views
enrichment to common gene
GeneSetEnrichment
genes
genetogo
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 years ago by
Noy
• 0
12
votes
13
replies
12k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 15 months ago by
ATpoint
★ 4.8k • written 3.2 years ago by
nhaus
▴ 70
1
vote
0
replies
1.9k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
3.6 years ago
makrez
▴ 10
3
votes
2
replies
1.8k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 4.4 years ago by
Gordon Smyth
52k • written 4.4 years ago by
prabin.dm
• 0
0
votes
1
reply
1.8k
views
Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler
GeneSetEnrichment
enrichplot
updated 4.4 years ago by
Emilia
▴ 40 • written 4.4 years ago by
saw44
• 0
0
votes
0
replies
784
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
4.5 years ago
paun_bio
• 0
1
vote
4
replies
3.6k
views
Problem retrieving graphics in clusterprofiler
software error
clusterprofiler
GO
genesetenrichment
9.0 years ago
José Luis Lavín
▴ 10
1
vote
0
replies
1.3k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma
genesetenrichment
updated 9.2 years ago by
Steve Lianoglou
★ 13k • written 9.2 years ago by
Aditya
▴ 160
1
vote
0
replies
1.6k
views
News:
Announcing the EnrichmentBrowser 2.0
genesetenrichment
functional enrichment
enrichmentbrowser
News
9.3 years ago
Ludwig Geistlinger
▴ 70
5
votes
7
replies
5.8k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 9.4 years ago by
Gordon Smyth
52k • written 9.4 years ago by
Jon Bråte
▴ 270
2
votes
1
reply
1.3k
views
elim method for KEGG pathways?
KEGG
genesetenrichment
elim
updated 9.5 years ago by
James W. MacDonald
68k • written 9.5 years ago by
jacorvar
▴ 40
2
votes
2
replies
2.3k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 9.7 years ago by
Nadia Davidson
▴ 320 • written 9.7 years ago by
xyliu00
▴ 20
8
votes
14
replies
4.7k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 10.1 years ago by
willem.ligtenberg
▴ 150 • written 10.5 years ago by
Guangchuang Yu
★ 1.2k
1
vote
1
reply
5.9k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 10.3 years ago by
Luo Weijun
★ 1.6k • written 10.3 years ago by
Alan Smith
▴ 150
0
votes
0
replies
1.3k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
10.4 years ago
Peter.Wood
• 0
0
votes
0
replies
1.9k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
10.5 years ago
Guangchuang Yu
★ 1.2k
0
votes
3
replies
2.1k
views
Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 11.1 years ago by
Steve Lianoglou
★ 13k • written 11.1 years ago by
Leif Väremo
▴ 70
31 results • Page
1 of 1
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Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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