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go
•
reset
0
votes
0
replies
54
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
5 days ago
danalvoronov
▴ 10
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
0
votes
1
reply
292
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 11 weeks ago by
belinda.phipson
▴ 40 • written 11 weeks ago by
s.malik
• 0
1
vote
3
replies
393
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Tyler Sagendorf
▴ 10
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
0
votes
2
replies
472
views
GO enrichment analysis does not show any pathways in my case
GO
EnrichmentBrowser
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
prity6459
• 0
0
votes
4
replies
593
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO
ensembldb
7 months ago
Rockbar
• 0
1
vote
1
reply
440
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 8 months ago by
James W. MacDonald
66k • written 8 months ago by
Alvin
• 0
0
votes
1
reply
639
views
Trouble using biomaRt to pull pathway genes from GO
GO
biomaRt
updated 10 months ago by
James W. MacDonald
66k • written 10 months ago by
cstorer
• 0
0
votes
0
replies
470
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
13 months ago
Priya
• 0
0
votes
2
replies
9.0k
views
Clusterprofiler error: No gene can be mapped
software error
go
annotation
clusterProfiler
updated 13 months ago by
tarltonuk2089
• 0 • written 4.1 years ago by
tianshenbio
• 0
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
0
votes
2
replies
2.6k
views
Using biomaRt for getting Go Terms
GO
biomaRt
GO
biomaRt
updated 13 months ago by
Divya
• 0 • written 13.4 years ago by
chawla
▴ 190
0
votes
2
replies
779
views
GO analysis in R vs website
GO
RNASeq
14 months ago
Nitro
• 0
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
1
vote
4
replies
1.2k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db
GO
msigdbr
15 months ago
S
▴ 10
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
1
vote
1
reply
1.1k
views
topGo error loading data
topGO
GO
17 months ago
peter
• 0
2
votes
4
replies
2.2k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 18 months ago by
abhisek001
• 0
0
votes
1
reply
616
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 18 months ago by
Laia
▴ 10 • written 18 months ago by
acram
• 0
0
votes
1
reply
700
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db
GOfuncR
GO
GOSim
goProfiles
updated 19 months ago by
Basti
▴ 780 • written 19 months ago by
yeluo
• 0
0
votes
0
replies
543
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO
GeneOntology
LocusIDtogeneIDconversion
19 months ago
BioinFo.X
• 0
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
20 months ago • updated 19 months ago
dario.beraldi
• 0
2
votes
3
replies
2.3k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi
GO
clusterProfiler
enrichplot
ensembldb
updated 20 months ago by
merv
▴ 120 • written 20 months ago by
simone.nevills
▴ 10
0
votes
3
replies
4.9k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 23 months ago by
pengmin.wang.1
• 0 • written 12.2 years ago by
Marc Carlson
★ 7.2k
0
votes
4
replies
3.4k
views
How to combine VCF-class and data.frame with annotations
GO
annotate
convert
ggbio
GO
annotate
convert
ggbio
written 11.7 years ago by
Stefan Dentro
▴ 70
1
vote
3
replies
1.7k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 23 months ago by
James W. MacDonald
66k • written 23 months ago by
Raito92
▴ 60
0
votes
13
replies
2.9k
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 2.0 years ago by
Guido Hooiveld
★ 4.0k • written 2.0 years ago by
Lucía
▴ 10
0
votes
1
reply
2.1k
views
Registration Confirmation
GO
GO
updated 2.1 years ago by
Pavlo
• 0 • written 14.5 years ago by
matchmail@connect.match.com
▴ 10
0
votes
0
replies
600
views
What exactly are Nontrivial node in topGO analysis?
topGO
GO
2.1 years ago
theophile
• 0
0
votes
0
replies
3.0k
views
Create a Gene Enrichment GO plot from goana output
goana
RNASeq
edgeR
RnaSeq
GO
2.2 years ago
Raito92
▴ 60
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
1
vote
2
replies
1.2k
views
Gene Onotology: Can't get the goana function to work
edgeR
GO
2.2 years ago
Adelyn
▴ 10
0
votes
1
reply
1.3k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 2.3 years ago by
Kevin Blighe
★ 3.9k • written 2.3 years ago by
Omurice
• 0
0
votes
3
replies
1.8k
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 2.3 years ago by
Gordon Smyth
50k • written 2.3 years ago by
David R
▴ 90
2
votes
3
replies
1.7k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats
GO
RNASeq
updated 2.5 years ago by
James W. MacDonald
66k • written 2.5 years ago by
joasmile84
▴ 20
2
votes
6
replies
1.4k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO
biomaRt
updated 2.8 years ago by
Mike Smith
★ 6.5k • written 2.8 years ago by
A
• 0
0
votes
1
reply
754
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq
GO
updated 3.0 years ago by
James W. MacDonald
66k • written 3.0 years ago by
Yosapol
• 0
2
votes
2
replies
1.0k
views
retrieve gene IDs from GO.db GO
GO
GO.db
3.0 years ago
decppced
• 0
0
votes
9
replies
1.8k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO
biomartr
annotation
ensemble
fungi
updated 3.0 years ago by
James W. MacDonald
66k • written 3.1 years ago by
Bettina
• 0
2
votes
2
replies
2.7k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
3.2 years ago
Wuschel
▴ 10
2
votes
0
replies
954
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.3 years ago
Ben
▴ 50
2
votes
1
reply
1.9k
views
topGO expected values showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 3.3 years ago by
Doc
▴ 20 • written 11.2 years ago by
Kishor Tappita
▴ 340
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.5 years ago by
James W. MacDonald
66k • written 3.5 years ago by
ojong
• 0
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error
topGO
go
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
maria.ratto
• 0
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
0
votes
0
replies
618
views
ViseaGO merge_enrich_terms ERROR
go
3.9 years ago
zaza.inline
• 0
0
votes
9
replies
1.6k
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
3.9 years ago
camillab.
▴ 10
2
votes
2
replies
891
views
biomart webservice error when using data from Phytozome
software error
go
3.9 years ago
e.lopez-cortegano
• 0
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler
GO
3.9 years ago
Ruixuan
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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