Showing : go • reset
0
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0
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48
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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 • 0 • written 6.4 years ago by ▴ 20
0
votes
1
reply
290
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 11 weeks ago by ▴ 40 • written 11 weeks ago by • 0
1
vote
3
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391
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 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 ★ 4.0k • written 3.3 years ago by • 0
0
votes
2
replies
469
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 3 months ago by 65k • written 3 months ago by • 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 65k • written 8 months ago by • 0
0
votes
1
reply
638
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
0
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467
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
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9.0k
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
updated 13 months ago by • 0 • written 4.1 years ago by • 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
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2.6k
views
Using biomaRt for getting Go Terms
GO biomaRt GO biomaRt
updated 13 months ago by • 0 • written 13.4 years ago by ▴ 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
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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 65k • written 4.0 years ago by ▴ 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 17 months ago by • 0
0
votes
1
reply
616
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 18 months ago by ▴ 10 • written 18 months ago by • 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 ▴ 780 • written 19 months ago by • 0
0
votes
0
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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
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 ▴ 120 • written 20 months ago by ▴ 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 • 0 • written 12.2 years ago by ★ 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 ▴ 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 65k • written 23 months ago by ▴ 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 ★ 4.0k • written 2.0 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Registration Confirmation
GO GO
updated 2.1 years ago by • 0 • written 14.5 years ago by ▴ 10
0
votes
0
replies
599
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
2.1 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
3.4k
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 50k • written 2.2 years ago by ▴ 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 ★ 3.9k • written 2.3 years ago by • 0
0
votes
3
replies
1.8k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2.3 years ago by 50k • written 2.3 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 2.5 years ago by 65k • written 2.5 years ago by ▴ 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 ★ 6.5k • written 2.8 years ago by • 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 65k • written 3.0 years ago by • 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 65k • written 3.1 years ago by • 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
953
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 ▴ 20 • written 11.2 years ago by ▴ 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 65k • written 3.5 years ago by • 0
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error topGO go
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
4
votes
1
reply
6.1k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 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
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
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 65k
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 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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