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go enrichment
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2.2k
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GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
4.6 years ago
Raito92
▴ 60
0
votes
0
replies
999
views
GOSemSim - slow for BP terms
gosemsim
go enrichment
go semantic similarity
5.4 years ago
nooshin
▴ 300
2
votes
6
replies
1.9k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
jgg
• 0
0
votes
1
reply
2.4k
views
Different results come from GO enrichment analysis with ENSEMBL ID and ENTREZID as keyTypes
clusterprofiler
go enrichment
functional enrichment
updated 5.5 years ago by
Guangchuang Yu
★ 1.2k • written 5.5 years ago by
Jack
• 0
0
votes
1
reply
1.2k
views
TopGO ks test using a score different from p-value
topgo
ks
score
kolmogorov-smirnov test
go enrichment
updated 5.9 years ago by
Lluís Revilla Sancho
▴ 730 • written 5.9 years ago by
eagomezc
• 0
0
votes
0
replies
940
views
GOseq No Underrepresented Categories
goseq
go enrichment
5.9 years ago
mart1139
• 0
1
vote
1
reply
1.5k
views
enrichGO (clusterProfiler) produces different results
chipseq
go enrichment
clusterprofiler
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
Javier Pérez Florido
▴ 840
0
votes
2
replies
3.7k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
josef.oeckl
• 0
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 7 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
3
votes
8
replies
2.1k
views
How does the org.Dm.eg.db package deal with NOT annotation qualifiers when annotating genes to GO?
org.dm.eg.db
gene ontology
go enrichment
annotation
NOT
updated 7.1 years ago by
Valerie Obenchain
★ 6.8k • written 7.2 years ago by
triZZla
• 0
0
votes
1
reply
1.1k
views
TopGO Drosophila ananassae
go enrichment
topgo
d.ananassae
updated 7.8 years ago by
James W. MacDonald
65k • written 7.8 years ago by
koeniger
▴ 10
3
votes
1
reply
2.1k
views
Tools for GO term enrichment in prokaryotes
bacteria
GO enrichment
updated 8.8 years ago by
Marc Carlson
★ 7.2k • written 8.8 years ago by
ksw
▴ 20
12 results • Page
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Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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