Showing : GO • reset
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93
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
4 weeks ago danalvoronov ▴ 10
4
votes
4
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3.9k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 12 weeks ago by • 0 • written 6.5 years ago by ▴ 20
0
votes
1
reply
355
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 3 months ago by ▴ 40 • written 3 months ago by • 0
1
vote
3
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446
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 4 months ago by 51k • written 4 months ago by ▴ 10
0
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2
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575
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 4 months ago by 66k • written 4 months ago by • 0
0
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4
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625
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
7 months ago Rockbar • 0
1
vote
1
reply
485
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 8 months ago by 66k • written 8 months ago by • 0
0
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1
reply
663
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 11 months ago by 66k • written 11 months ago by • 0
0
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0
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490
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
14 months ago Priya • 0
0
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2
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829
views
GO analysis in R vs website
GO RNASeq
15 months ago Nitro • 0
1
vote
4
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1.3k
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
1
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1
reply
1.1k
views
topGo error loading data
topGO GO
18 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 • 0
0
votes
1
reply
633
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 19 months ago by ▴ 10 • written 19 months ago by • 0
0
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1
reply
721
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 20 months ago by ▴ 780 • written 20 months ago by • 0
0
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0
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576
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
20 months ago BioinFo.X • 0
0
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4
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1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
20 months ago dario.beraldi • 0
2
votes
3
replies
2.4k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 20 months ago by ▴ 120 • written 20 months ago by ▴ 10
1
vote
3
replies
1.8k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 23 months ago by 66k • written 24 months ago by ▴ 60
0
votes
13
replies
3.0k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 2.1 years ago by ★ 4.0k • written 2.1 years ago by ▴ 10
0
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0
replies
618
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
2.2 years ago theophile • 0
0
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0
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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
3.5k
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 51k • written 2.2 years ago by ▴ 60
1
vote
2
replies
1.3k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
2.3 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 2.4 years ago by ★ 3.9k • written 2.4 years ago by • 0
0
votes
3
replies
1.8k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2.4 years ago by 51k • written 2.4 years ago by ▴ 90
2
votes
3
replies
1.7k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 2.6 years ago by 66k • written 2.6 years ago by ▴ 20
2
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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 ★ 6.5k • written 2.8 years ago by • 0
0
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1
reply
768
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 3.1 years ago by 66k • written 3.1 years ago by • 0
2
votes
2
replies
1.0k
views
retrieve gene IDs from GO.db GO
GO GO.db
3.1 years ago decppced • 0
0
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9
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1.8k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 3.1 years ago by 66k • written 3.1 years ago by • 0
2
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2
replies
2.8k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
3.3 years ago Wuschel ▴ 10
3
votes
11
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5.2k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 4 months ago by ★ 4.0k • written 3.4 years ago by • 0
2
votes
0
replies
976
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.4 years ago Ben ▴ 50
2
votes
1
reply
2.0k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 3.4 years ago by ▴ 20 • written 11.3 years ago by ▴ 340
2
votes
2
replies
1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.5 years ago by 66k • written 3.5 years ago by • 0
2
votes
3
replies
1.2k
views
Error in topGO analysis
software error topGO go
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by • 0
4
votes
1
reply
6.3k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 3.9 years ago by 66k • written 3.9 years ago by ▴ 30
0
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0
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627
views
ViseaGO merge_enrich_terms ERROR
go
4.0 years ago zaza.inline • 0
0
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9
replies
1.7k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.0 years ago camillab. ▴ 10
2
votes
2
replies
907
views
biomart webservice error when using data from Phytozome
software error go
4.0 years ago e.lopez-cortegano • 0
1
vote
5
replies
1.2k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
4.0 years ago Ruixuan ▴ 10
0
votes
1
reply
828
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 10
4
votes
8
replies
2.3k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 16 months ago by 66k • written 4.0 years ago by ▴ 30
0
votes
5
replies
1.3k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
4.1 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
929
views
About topGO error
go
updated 4.1 years ago by ▴ 30 • written 4.1 years ago by • 0
2
votes
4
replies
1.5k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
4.1 years ago liz.marjory • 0
0
votes
2
replies
749
views
GO analysis without gene IDs?
deseq2 annotation go
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 60
0
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0
replies
633
views
enrichplot pakage no output plot
go
4.1 years ago Hamidreza Hashemi ▴ 20
2
votes
1
reply
5.4k
views
GO of clusterprofiler
go
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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