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go
•
reset
15
votes
18
replies
3.4k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
Raito92
▴ 60
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.3 years ago by
Bernd Klaus
▴ 610 • written 9.3 years ago by
nw328
▴ 20
7
votes
9
replies
3.1k
views
GSEABase - View/extract GO terms mapped to each GOslim
go
GSEABase
GOslim
gene ontology
4.3 years ago • updated 13 months ago
samwhite
▴ 20
6
votes
6
replies
2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go
DE
edger
rnaseq
glmTreat
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
Raito92
▴ 60
5
votes
1
reply
1.3k
views
topGO under-representation table
topGO
GO
7.3 years ago • updated 7.2 years ago
beachboarder900
▴ 40
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 830
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
Raito92
▴ 60
5
votes
7
replies
4.9k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Jon Bråte
▴ 250
5
votes
4
replies
2.8k
views
biomaRT GO-ID retreival showing different genes than AmiGO
biomart
go
updated 7.4 years ago by
Mike Smith
★ 6.5k • written 7.4 years ago by
snamjoshi87
▴ 40
5
votes
2
replies
1.8k
views
How to get genes within a GO category of 'GOstat' results?
GO
updated 9.4 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Bade
▴ 310
4
votes
1
reply
6.1k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 3.9 years ago by
James W. MacDonald
66k • written 3.9 years ago by
adR
▴ 30
4
votes
3
replies
2.8k
views
Select the annotation level during GO enrichment
topgo
gostats
go
updated 9.6 years ago by
James W. MacDonald
66k • written 9.7 years ago by
artur
▴ 80
4
votes
1
reply
1.8k
views
Retrieving all genes related a go term
go
R
annotationdbi
biomart
updated 6.7 years ago by
James W. MacDonald
66k • written 6.7 years ago by
Stane
▴ 40
4
votes
1
reply
2.3k
views
Gene Ontology: filtering out most informative terms from a list of GO terms
GO
graph
GO
graph
updated 13.6 years ago by
Marc Carlson
★ 7.2k • written 13.6 years ago by
Aaron Weimann
▴ 30
4
votes
3
replies
2.5k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 9.5 years ago by
dalloliogm
▴ 50 • written 9.8 years ago by
Georg Otto
▴ 120
4
votes
8
replies
2.2k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 15 months ago by
James W. MacDonald
66k • written 4.0 years ago by
morteza.aslanzadeh
▴ 30
4
votes
3
replies
4.8k
views
Use R/Bioconductor to match BLAST hits to GO terms?
GO
BLAST
annotation
updated 9.6 years ago by
Marc Carlson
★ 7.2k • written 9.6 years ago by
Jon Bråte
▴ 250
4
votes
2
replies
2.6k
views
error with display of significant nodes using topGO
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 14.7 years ago by
Adrian Alexa
▴ 400 • written 14.7 years ago by
Kishor Tappita
▴ 340
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO
gage
goseq
KEGG
updated 9.6 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Merienne Nicolas
▴ 120
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 8 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
4
votes
1
reply
8.7k
views
WGCNA-unable to install GO.db package
go
cancer
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
852108577
▴ 20
3
votes
3
replies
8.7k
views
error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()
annotationforge
Annotation
GO
updated 9.7 years ago by
Marc Carlson
★ 7.2k • written 9.7 years ago by
artur
▴ 80
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.7 years ago
artur
▴ 80
3
votes
4
replies
1.5k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase
go
gene ontology
goslim
4.3 years ago • updated 14 months ago
samwhite
▴ 20
3
votes
1
reply
1.3k
views
ComBat crash/problem
GO
GO
updated 9.4 years ago by
yousefj
▴ 10 • written 10.0 years ago by
Peter Langfelder
★ 3.0k
3
votes
4
replies
3.9k
views
How to retrieve all GO terms at level 5 as well as their annotated genes
GO
GO
10.9 years ago
Peter Davidsen
▴ 210
3
votes
3
replies
1.2k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.9 years ago by
James W. MacDonald
66k • written 4.9 years ago by
t.bergmann
• 0
3
votes
5
replies
1.7k
views
GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
GO
bioclite
R3.5
mac os x
annotationdbi
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
Jens Preussner
▴ 30
3
votes
3
replies
1.4k
views
Getting genes list associated to current GO terms
biomart
go
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Stane
▴ 40
3
votes
3
replies
3.7k
views
how to find ensembl genes belonging to a GO category?
biomart
gene ontology
GO
updated 5.6 years ago by
James W. MacDonald
66k • written 5.6 years ago by
Guido Hooiveld
★ 4.0k
3
votes
11
replies
5.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 3.3 years ago by
Alberto
• 0
3
votes
3
replies
1.1k
views
source of GO ontology and GO annotations in Bioconductor for GO.db
GO
ontology
GO.db
updated 5.7 years ago by
apkmirrorproject
• 0 • written 5.7 years ago by
marcinjoachimiak
▴ 10
2
votes
1
reply
2.7k
views
topGO: how to visualize gene in GO enriched categories?
GO
updated 9.7 years ago by
Bernd Klaus
▴ 610 • written 9.7 years ago by
artur
▴ 80
2
votes
4
replies
3.3k
views
How to get list of all GOIDs with all genes in each GO term?
go
annotation
updated 4.2 years ago by
James W. MacDonald
66k • written 4.2 years ago by
theodore.killian
• 0
2
votes
11
replies
3.2k
views
R gives error when trying to install EnsDb.Hsapiens.v75 package
go
updated 4.6 years ago by
James W. MacDonald
66k • written 4.6 years ago by
desara.gora
• 0
2
votes
2
replies
8.0k
views
package built under R version 3.1.0 warning
GO
GO
updated 10.5 years ago by
Marc Carlson
★ 7.2k • written 10.5 years ago by
Diego Diez
▴ 760
2
votes
2
replies
2.1k
views
Converting single GRanges object as per chromosome GRangeList
SNP
GO
convert
SNP
GO
convert
updated 10.5 years ago by
Steve Lianoglou
★ 13k • written 10.5 years ago by
Prashantha Hebbar
▴ 260
2
votes
1
reply
5.3k
views
GO of clusterprofiler
go
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
doaa.mohamed
• 0
2
votes
2
replies
2.9k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq
ensemblid
GO
updated 5.5 years ago by
James W. MacDonald
66k • written 5.5 years ago by
mico
• 0
2
votes
1
reply
1.8k
views
medain global normalize - argument matrix
Normalization
GO
Normalization
GO
updated 11.5 years ago by
Gordon Smyth
50k • written 11.6 years ago by
James W. MacDonald
66k
2
votes
1
reply
1.2k
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 6.3 years ago by
James W. MacDonald
66k • written 6.3 years ago by
lehallib
• 0
2
votes
2
replies
1.1k
views
How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?
GO
Homo sapiens
GO
Homo sapiens
updated 11.8 years ago by
Marc Carlson
★ 7.2k • written 11.8 years ago by
Peng Yu
▴ 940
2
votes
0
replies
1.4k
views
Problem using Rgraphviz (edge weights going missing).
GO
graph
Rgraphviz
GO
graph
Rgraphviz
15.6 years ago
Dan Bolser
▴ 40
2
votes
5
replies
1.3k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment
GO
Cancer
BSgenome
BSgenome
Alignment
GO
Cancer
BSgenome
BSgenome
updated 10.9 years ago by
Martin Morgan
25k • written 10.9 years ago by
Guest User
★ 13k
2
votes
0
replies
1.1k
views
automating makeContrasts call in limma
GO
GO
18.0 years ago
Greg Finak
▴ 50
2
votes
7
replies
6.6k
views
GO.db installation error
go
sqlite
updated 8.4 years ago by
Daniel Lai
• 0 • written 8.5 years ago by
predeus
• 0
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
6.8 years ago
cabezasdelafuented
▴ 10
2
votes
2
replies
1.3k
views
How to remove IEA genes from list of GO terms?
go
annotation
organismdb
updated 9.6 years ago by
James W. MacDonald
66k • written 9.6 years ago by
Guido Hooiveld
★ 4.0k
2
votes
8
replies
2.0k
views
Genes annotated to GO:0031281 using org.Hs.eg.db
GO
Homo sapiens
GO
Homo sapiens
updated 10.2 years ago by
James W. MacDonald
66k • written 10.2 years ago by
Tim Smith
★ 1.1k
2
votes
2
replies
2.1k
views
GO offspring consistency
annotation
GO
graph
gene ontology
updated 9.4 years ago by
Laurent Gatto
1.6k • written 9.5 years ago by
jelle.goeman
• 0
50 results • Page
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Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
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Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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