Showing : go • reset
0
votes
0
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80
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
14 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 10 weeks ago by • 0 • written 6.5 years ago by ▴ 20
0
votes
1
reply
317
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 12 weeks ago by ▴ 40 • written 12 weeks ago by • 0
1
vote
3
replies
402
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
510
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
votes
4
replies
594
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
7 months ago Rockbar • 0
1
vote
1
reply
457
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 8 months ago by 66k • written 8 months ago by • 0
0
votes
1
reply
646
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 10 months ago by 66k • written 10 months ago by • 0
0
votes
0
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475
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
9.1k
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 14 months ago samwhite ▴ 20
0
votes
2
replies
2.6k
views
Using biomaRt for getting Go Terms
GO biomaRt GO biomaRt
updated 14 months ago by • 0 • written 13.4 years ago by ▴ 190
0
votes
2
replies
791
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 16 months ago by 66k • 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 18 months ago by • 0
0
votes
1
reply
621
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
707
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
votes
0
replies
556
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
20 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 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 12.3 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 11.8 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 66k • 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
604
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
3.5k
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 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 66k • 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
758
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 3.0 years ago by 66k • written 3.0 years ago by • 0
2
votes
2
replies
1.0k
views
retrieve gene IDs from GO.db GO
GO GO.db
3.1 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 3.1 years ago by 66k • 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
3.3 years ago Wuschel ▴ 10
2
votes
0
replies
958
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 3.4 years ago by ▴ 20 • written 11.2 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
1.1k
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
6.2k
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
votes
0
replies
619
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
894
views
biomart webservice error when using data from Phytozome
software error go
4.0 years ago e.lopez-cortegano • 0
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
4.0 years ago Ruixuan ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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