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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
updated 3 days ago by 68k • written 5 days ago by ▴ 10
7
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9
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1.5k
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clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
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2
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629
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Question on number of genes used in GO analysis
GO clusterProfiler
8 months ago Danté • 0
0
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0
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345
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
11 months ago danalvoronov ▴ 10
4
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4
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4.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 13 months ago by • 0 • written 7.4 years ago by ▴ 20
1
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3
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1.9k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
13 months ago • updated 7 months ago s.malik • 0
1
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3
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1.2k
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 14 months ago by 52k • written 14 months ago by ▴ 10
0
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2
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1.9k
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GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 15 months ago by 68k • written 15 months ago by • 0
0
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4
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1.3k
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Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
18 months ago Rockbar • 0
1
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3
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1.1k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 3 months ago by 68k • written 19 months ago by • 0
0
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1
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967
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 21 months ago by 68k • written 21 months ago by • 0
0
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0
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721
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.0 years ago Priya • 0
0
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2
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1.3k
views
GO analysis in R vs website
GO RNASeq
2.1 years ago Nitro • 0
1
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4
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2.2k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
2.2 years ago S ▴ 10
1
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1
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1.8k
views
topGo error loading data
topGO GO
2.3 years ago peter • 0
2
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4
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3.2k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 2.4 years ago by • 0
0
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1
reply
898
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 2.5 years ago by ▴ 10 • written 2.5 years ago by • 0
0
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1
reply
954
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 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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0
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758
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Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
2.6 years ago BioinFo.X • 0
0
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4
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1.5k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
2.6 years ago dario.beraldi • 0
2
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3
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3.5k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.6 years ago by ▴ 150 • written 2.6 years ago by ▴ 10
1
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3
replies
2.9k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 60
0
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13
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4.1k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by ▴ 30
0
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0
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807
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.0 years ago theophile • 0
0
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0
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3.9k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.1 years ago Raito92 ▴ 60
15
votes
18
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4.6k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.1 years ago by 52k • written 3.1 years ago by ▴ 60
1
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2
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1.8k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.1 years ago Adelyn ▴ 10
0
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1
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1.7k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
0
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3
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2.5k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.2 years ago by 52k • written 3.2 years ago by ▴ 90
2
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3
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2.3k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 20
2
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6
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1.9k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 3.7 years ago by ★ 6.6k • written 3.7 years ago by • 0
0
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1
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989
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
2
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2
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1.3k
views
retrieve gene IDs from GO.db GO
GO GO.db
4.0 years ago decppced • 0
0
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9
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2.3k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
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2
replies
3.4k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
4.2 years ago Wuschel ▴ 10
3
votes
11
replies
6.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 14 months ago by ★ 4.1k • written 4.2 years ago by • 0
2
votes
0
replies
1.3k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.2 years ago Ben ▴ 50
2
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1
reply
2.3k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.3 years ago by ▴ 20 • written 12.1 years ago by ▴ 340
2
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2
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1.5k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
2
votes
3
replies
1.5k
views
Error in topGO analysis
software error topGO go
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
4
votes
1
reply
8.8k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 40
0
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0
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767
views
ViseaGO merge_enrich_terms ERROR
go
4.8 years ago zaza.inline • 0
0
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9
replies
2.2k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.8 years ago camillab. ▴ 10
2
votes
2
replies
1.3k
views
biomart webservice error when using data from Phytozome
software error go
4.9 years ago e.lopez-cortegano • 0
1
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5
replies
1.6k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
4.9 years ago Ruixuan ▴ 10
0
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1
reply
1.1k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
4
votes
8
replies
3.0k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.2 years ago by 68k • written 4.9 years ago by ▴ 30
0
votes
5
replies
1.8k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
4.9 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
1.2k
views
About topGO error
go
updated 5.0 years ago by ▴ 30 • written 5.0 years ago by • 0
2
votes
4
replies
1.9k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
5.0 years ago liz.marjory • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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