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GO enrichment
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0
votes
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1.4k
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GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
3.4 years ago
Raito92
▴ 60
0
votes
0
replies
673
views
GOSemSim - slow for BP terms
gosemsim
go enrichment
go semantic similarity
4.2 years ago
nooshin
▴ 300
2
votes
6
replies
1.1k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 4.2 years ago by
James W. MacDonald
62k • written 4.2 years ago by
jgg
• 0
0
votes
1
reply
1.4k
views
Different results come from GO enrichment analysis with ENSEMBL ID and ENTREZID as keyTypes
clusterprofiler
go enrichment
functional enrichment
updated 4.2 years ago by
Guangchuang Yu
★ 1.2k • written 4.2 years ago by
Jack
• 0
0
votes
1
reply
822
views
TopGO ks test using a score different from p-value
topgo
ks
score
kolmogorov-smirnov test
go enrichment
updated 4.6 years ago by
Lluís Revilla Sancho
▴ 700 • written 4.6 years ago by
eagomezc
• 0
0
votes
0
replies
604
views
GOseq No Underrepresented Categories
goseq
go enrichment
4.6 years ago
mart1139
• 0
1
vote
1
reply
952
views
enrichGO (clusterProfiler) produces different results
chipseq
go enrichment
clusterprofiler
updated 4.9 years ago by
Guangchuang Yu
★ 1.2k • written 4.9 years ago by
Javier Pérez Florido
▴ 840
0
votes
2
replies
2.8k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 5.0 years ago by
Michael Love
39k • written 5.0 years ago by
josef.oeckl
• 0
4
votes
3
replies
2.5k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 7 months ago by
pengmin.wang.1
• 0 • written 5.1 years ago by
Huang, Lei [BSD] - CRI
▴ 20
3
votes
8
replies
1.5k
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 5.9 years ago by
Valerie Obenchain
★ 6.7k • written 5.9 years ago by
ivozeller
• 0
0
votes
1
reply
800
views
TopGO Drosophila ananassae
go enrichment
topgo
d.ananassae
updated 6.6 years ago by
James W. MacDonald
62k • written 6.6 years ago by
koeniger
▴ 10
3
votes
1
reply
1.6k
views
Tools for GO term enrichment in prokaryotes
bacteria
GO enrichment
updated 7.5 years ago by
Marc Carlson
★ 7.2k • written 7.5 years ago by
ksw
▴ 20
12 results • Page
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Comment: mas5calls function doesn't work; mirna40cdf problem
by
Guido Hooiveld
★ 3.5k
Also: you could consider using `DABG` for present/absent calls. James elaborated on this in this thread: https://support.bioconductor.org/p…
Comment: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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