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topGO
•
reset
0
votes
0
replies
1.1k
views
TopGO Analysis of gene enrichment - enriched terms are not in the original list
topgo
9.2 years ago
pninasmail
• 0
3
votes
4
replies
2.2k
views
Trying to account for gene length in topGO analysis
topgo
goseq
deseq2
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 years ago by
Ben Mansfeld
• 0
0
votes
4
replies
1.6k
views
GO annotation and gene set testing for plant dataset
go
edger
annotation
topgo
bioconductor
9.3 years ago
myprogramming2016
• 0
0
votes
3
replies
4.5k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo
biomart
gene ontology
goexpress
pathway analysis
updated 9.3 years ago by
kevin.rue
▴ 350 • written 9.3 years ago by
Darya Vanichkina
▴ 130
0
votes
1
reply
2.1k
views
Gene Set Enrichment Analysis with topGO
topGO
gene set analysis
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
jacorvar
▴ 40
13
votes
2
replies
5.3k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 9.8 years ago by
Robert Castelo
★ 3.4k • written 9.8 years ago by
jacorvar
▴ 40
0
votes
1
reply
1.6k
views
topGO circles in the graph
topgo
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
carmen.leida
• 0
1
vote
4
replies
2.1k
views
Obsolete GO terms in topGO analysis
topgo
9.9 years ago
s.apocarpum
▴ 10
3
votes
2
replies
2.6k
views
How to use TopGO with gene symbols extracted from Illumina probes
topgo
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
Ahdee
▴ 60
0
votes
0
replies
1.5k
views
GO enrichment analysis Vs GO slims enrichment analysis
topgo
9.9 years ago
s.apocarpum
▴ 10
5
votes
2
replies
2.4k
views
What is Nontrivial node in topGO analysis?
topgo
updated 10.1 years ago by
James W. MacDonald
68k • written 10.1 years ago by
s.apocarpum
▴ 10
0
votes
1
reply
1.2k
views
Understanding of "feasible genes" conception
topgo
10.1 years ago
s.apocarpum
▴ 10
0
votes
1
reply
986
views
GO-term comparison between two genomic regions
topgo
GO
annotation
updated 10.1 years ago by
James W. MacDonald
68k • written 10.1 years ago by
austrius
• 0
1
vote
2
replies
1.7k
views
Absence of GO terms for some genes of interest in topGO package
topgo
updated 10.1 years ago by
James W. MacDonald
68k • written 10.1 years ago by
s.apocarpum
▴ 10
0
votes
1
reply
2.7k
views
How to use org.Mm.eg.db as chip in topGO printGenes function
topgo
org.mm.eg.db
updated 10.1 years ago by
fletchkatie
• 0 • written 10.3 years ago by
komalr
• 0
3
votes
0
replies
2.0k
views
Interpret topGO reults
topGO
reults
10.2 years ago
megerdes
▴ 40
4
votes
3
replies
2.6k
views
topGO error "No function to select the significant genes provided!"
topgo
updated 10.3 years ago by
James W. MacDonald
68k • written 10.3 years ago by
megerdes
▴ 40
4
votes
3
replies
4.6k
views
topGO: significant genes in GO enriched categories
topGO
updated 10.4 years ago by
lidia.mateo
▴ 30 • written 10.5 years ago by
samuel collombet
▴ 140
1
vote
1
reply
2.2k
views
topGO - genesInTerm returns genes not in the annotation
topGO
10.5 years ago
samuel collombet
▴ 140
0
votes
7
replies
4.4k
views
Error in loading R package topgo
topgo
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
vjimenez
• 0
0
votes
4
replies
3.3k
views
topGO annotations issue
topgo
annotationdbi
10.6 years ago
willmacnair
• 0
0
votes
1
reply
2.4k
views
topGO: genes annotated to a significant GO term
topGO
10.6 years ago
Brian Smith
▴ 120
0
votes
1
reply
5.6k
views
topGO: How to create gene2GO annotation for mouse?
topgo
updated 10.6 years ago by
Bernd Klaus
▴ 610 • written 10.6 years ago by
Brian Smith
▴ 120
1
vote
1
reply
6.0k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 10.6 years ago by
Luo Weijun
★ 1.6k • written 10.6 years ago by
Alan Smith
▴ 150
0
votes
3
replies
2.9k
views
topGO - Two-tailed (depletion/enrichment) analysis?
topgo
go
updated 10.7 years ago by
Gordon Smyth
53k • written 10.7 years ago by
nk
▴ 10
8
votes
16
replies
7.4k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 10.8 years ago by
Levi Waldron
★ 1.1k • written 10.8 years ago by
kaushal Raj Chaudhary
▴ 10
4
votes
3
replies
3.8k
views
Select the annotation level during GO enrichment
topgo
gostats
go
updated 11.0 years ago by
James W. MacDonald
68k • written 11.0 years ago by
artur
▴ 80
0
votes
1
reply
1.7k
views
Trouble installing topGO package
topGO
11.0 years ago
Eric Fournier
▴ 40
0
votes
1
reply
2.1k
views
topGO
topGO
topGO
updated 11.1 years ago by
James W. MacDonald
68k • written 11.1 years ago by
Steven Stadler
▴ 10
0
votes
2
replies
1.7k
views
Can my problem be addressed with Bioconductor?
Genetics
GOstats
SNPchip
topGO
Genetics
GOstats
SNPchip
topGO
updated 11.2 years ago by
James W. MacDonald
68k • written 11.2 years ago by
Guest User
★ 13k
0
votes
0
replies
1.5k
views
Please revise this edgeR code
Alignment
Organism
topGO
edgeR
Alignment
Organism
topGO
edgeR
11.4 years ago
biotech
▴ 160
0
votes
0
replies
1.7k
views
Is this edgeR code OK?
Alignment
Organism
topGO
edgeR
Alignment
Organism
topGO
edgeR
11.4 years ago
biotech
▴ 160
0
votes
0
replies
1.6k
views
Any COG enrichment tools?
GO
topGO
GO
topGO
11.5 years ago
biotech
▴ 160
0
votes
5
replies
2.6k
views
TopGo package
GO
topGO
GO
topGO
updated 11.5 years ago by
Dan Tenenbaum
★ 8.2k • written 11.5 years ago by
Qian Wang
▴ 20
0
votes
3
replies
2.7k
views
Find enriched GO terms, given a list of GO terms of interest and background GO terms
Annotation
GO
topGO
genomes
Annotation
GO
topGO
genomes
11.7 years ago
Guest User
★ 13k
0
votes
1
reply
1.4k
views
topGO spurious GO terms?
Pathways
GO
topGO
Pathways
GO
topGO
updated 11.7 years ago by
Jan T Kim
▴ 50 • written 11.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
New GO terms after TopGO enrichment? (updated)
GO
topGO
GO
topGO
updated 11.9 years ago by
biotech
▴ 160 • written 11.9 years ago by
Adrian Alexa
▴ 400
1
vote
0
replies
1.1k
views
New GO terms after TopGO enrichment? (updated)
GO
topGO
GO
topGO
11.9 years ago
biotech
▴ 160
0
votes
0
replies
1.2k
views
New GO terms after TopGO enrichment?
GO
topGO
GO
topGO
11.9 years ago
biotech
▴ 160
0
votes
1
reply
1.4k
views
topGO analysis returns different gene counts for category than given for non-model organism
Annotation
GO
topGO
Annotation
GO
topGO
updated 12.0 years ago by
Diana Toups Dugas
▴ 20 • written 12.0 years ago by
Adrian Alexa
▴ 400
0
votes
1
reply
1.7k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO
Category
topGO
GO
Category
topGO
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Diana Toups Dugas
▴ 20
0
votes
0
replies
2.5k
views
topgo GO mapping for non model organisms
Annotation
GO
Organism
topGO
Annotation
GO
Organism
topGO
12.1 years ago
km
▴ 100
1
vote
4
replies
4.9k
views
[topGO] More flexible way to select 'interesting' genes
GO
probe
topGO
GO
probe
topGO
updated 12.1 years ago by
Adrian Alexa
▴ 400 • written 12.1 years ago by
enricoferrero
▴ 680
0
votes
0
replies
895
views
topGO question
topGO
topGO
12.1 years ago
Datong Wang
▴ 10
2
votes
1
reply
1.4k
views
TopGO 0 nontrivial nodes
topGO
topGO
12.1 years ago
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.7k
views
topGO desperation
GO
topGO
GO
topGO
12.3 years ago
Oertlin, Christian Stud. FHML
▴ 20
0
votes
0
replies
1.4k
views
topGO expected value column showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
12.5 years ago
Kishor Tappita
▴ 340
0
votes
0
replies
1.5k
views
how to supply a vector/list of results to GenTable in topGO?
GO
PROcess
topGO
GO
PROcess
topGO
12.6 years ago
Adrian Alexa
▴ 400
0
votes
0
replies
1.0k
views
how to supply a vector/list of results to GenTable in topGO?
topGO
topGO
12.6 years ago
Aaron Mackey
▴ 170
1
vote
0
replies
1.2k
views
GO graphs made with topGO are unreadable
GO
graph
topGO
GO
graph
topGO
12.7 years ago
Guest User
★ 13k
211 results • Page
3 of 5
Recent ...
Replies
Comment: Heatmap of the Count Matrix
by
ArnulfoByrd
• 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics
by
James W. MacDonald
68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
by
James W. MacDonald
68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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