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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
994
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 5.8 years ago by
Lluís Revilla Sancho
▴ 730 • written 5.8 years ago by
eagomezc
• 0
0
votes
0
replies
936
views
GOseq No Underrepresented Categories
goseq
go enrichment
5.8 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
41k • written 6.2 years ago by
josef.oeckl
• 0
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 6 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 7.1 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 8.7 years ago by
Marc Carlson
★ 7.2k • written 8.7 years ago by
ksw
▴ 20
12 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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