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go enrichment
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2.1k
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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
992
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
2.3k
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
932
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
3.6k
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 5 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
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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