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GeneSetEnrichment
•
reset
2
votes
2
replies
708
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
3 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
544
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 5 months ago by
ATpoint
★ 4.6k • written 5 months ago by
picasa1983
• 0
0
votes
1
reply
750
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 7 months ago by
Guido Hooiveld
★ 4.1k • written 7 months ago by
aogunbaw
• 0
1
vote
2
replies
1.2k
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
8 months ago
Ana
• 0
0
votes
2
replies
582
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
8 months ago
Seongsu
• 0
4
votes
4
replies
4.4k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 9 months ago by
jandrade
• 0 • written 7.0 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
0
replies
563
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
17 months ago
sonal
• 0
0
votes
1
reply
1.5k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 17 months ago by
James W. MacDonald
67k • written 17 months ago by
manuelsokolov
• 0
0
votes
2
replies
4.8k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.5 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
9.6k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 10 months ago by
ATpoint
★ 4.6k • written 2.8 years ago by
nhaus
▴ 70
1
vote
0
replies
1.7k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
3.2 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 4.0 years ago by
Emilia
▴ 40 • written 4.0 years ago by
saw44
• 0
0
votes
0
replies
711
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
4.1 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 8.8 years ago by
Steve Lianoglou
★ 13k • written 8.8 years ago by
Aditya
▴ 160
1
vote
0
replies
1.5k
views
News:
Announcing the EnrichmentBrowser 2.0
genesetenrichment
functional enrichment
enrichmentbrowser
News
8.9 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 9.1 years ago by
James W. MacDonald
67k • written 9.1 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 10.1 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
1.9k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
10.1 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: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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Ali Barry
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gabriel.hoffman
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to
Jenny Drnevich
★ 2.0k
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to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
67k
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