Showing : go • reset
0
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
7 months ago • updated 6 months ago GA ▴ 10
7
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9
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2.0k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
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2
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861
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Question on number of genes used in GO analysis
GO clusterProfiler
15 months ago Danté • 0
0
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0
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494
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
18 months ago danalvoronov ▴ 10
4
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4
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5.2k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 20 months ago by • 0 • written 8.0 years ago by ▴ 20
1
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3
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2.2k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
21 months ago • updated 14 months ago s.malik • 0
1
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3
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1.5k
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 21 months ago by 53k • written 21 months ago by ▴ 10
0
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2
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2.3k
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GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 22 months ago by 68k • written 22 months ago by • 0
0
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4
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1.6k
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Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
2.1 years ago Rockbar • 0
1
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3
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1.5k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 10 months ago by 68k • written 2.2 years ago by • 0
0
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1
reply
1.2k
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Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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0
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852
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.6 years ago Priya • 0
0
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2
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1.6k
views
GO analysis in R vs website
GO RNASeq
2.7 years ago Nitro • 0
1
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4
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2.6k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
2.8 years ago S ▴ 10
1
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1
reply
2.0k
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topGo error loading data
topGO GO
2.9 years ago peter • 0
2
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4
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3.7k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 3.0 years ago by • 0
0
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1
reply
1.1k
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by • 0
0
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1
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1.1k
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 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
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0
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849
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Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
3.2 years ago BioinFo.X • 0
0
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4
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1.8k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
3.2 years ago dario.beraldi • 0
2
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3
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3.9k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 3.2 years ago by ▴ 150 • written 3.2 years ago by ▴ 10
1
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3
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3.2k
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Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 60
0
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13
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4.7k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by ▴ 30
0
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0
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962
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
3.6 years ago theophile • 0
0
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0
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4.3k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.7 years ago Raito92 ▴ 60
15
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18
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5.1k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
1
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2
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2.0k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.7 years ago Adelyn ▴ 10
0
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1
reply
2.0k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
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3
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2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 90
2
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3
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2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 20
2
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6
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2.1k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by • 0
0
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1
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1.1k
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
2
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2
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1.6k
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retrieve gene IDs from GO.db GO
GO GO.db
4.6 years ago decppced • 0
0
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9
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2.6k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
2
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2
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3.7k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
4.8 years ago Wuschel ▴ 10
3
votes
11
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7.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 22 months ago by ★ 4.1k • written 4.8 years ago by • 0
2
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0
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1.5k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.8 years ago Ben ▴ 50
2
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1
reply
2.5k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.9 years ago by ▴ 20 • written 12.7 years ago by ▴ 340
2
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2
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1.7k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
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3
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1.7k
views
Error in topGO analysis
software error topGO go
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
4
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1
reply
9.4k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 40
0
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0
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842
views
ViseaGO merge_enrich_terms ERROR
go
5.4 years ago zaza.inline • 0
0
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9
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2.5k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.4 years ago camillab. ▴ 10
2
votes
2
replies
1.4k
views
biomart webservice error when using data from Phytozome
software error go
5.4 years ago e.lopez-cortegano • 0
1
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5
replies
1.8k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
5.5 years ago Ruixuan ▴ 10
0
votes
1
reply
1.2k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
4
votes
8
replies
3.4k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.8 years ago by 68k • written 5.5 years ago by ▴ 30
0
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5
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2.1k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
5.5 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
1.3k
views
About topGO error
go
updated 5.6 years ago by ▴ 30 • written 5.6 years ago by • 0
2
votes
4
replies
2.1k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
5.6 years ago liz.marjory • 0
1,936 results • Page 1 of 39
Recent ...
Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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