Showing : go • reset
0
votes
1
reply
235
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 7 weeks ago by ▴ 40 • written 7 weeks ago by • 0
1
vote
3
replies
332
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
0
votes
2
replies
358
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
4
replies
540
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago Rockbar • 0
1
vote
1
reply
411
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
1
reply
606
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
0
replies
449
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
12 months ago Priya • 0
0
votes
2
replies
730
views
GO analysis in R vs website
GO RNASeq
13 months ago Nitro • 0
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
14 months ago S ▴ 10
1
vote
1
reply
1.0k
views
topGo error loading data
topGO GO
16 months ago peter • 0
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 17 months ago by • 0
0
votes
1
reply
592
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 17 months ago by ▴ 10 • written 17 months ago by • 0
0
votes
1
reply
675
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 18 months ago by ▴ 780 • written 18 months ago by • 0
0
votes
0
replies
514
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
18 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
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 19 months ago by ▴ 120 • written 19 months ago by ▴ 10
1
vote
3
replies
1.6k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 22 months ago by 65k • written 22 months ago by ▴ 60
0
votes
13
replies
2.8k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 23 months ago by ★ 3.9k • written 23 months ago by ▴ 10
0
votes
0
replies
579
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
2.0 years ago theophile • 0
0
votes
0
replies
2.9k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
2.1 years ago Raito92 ▴ 60
15
votes
18
replies
3.3k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 60
1
vote
2
replies
1.2k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
2.1 years ago Adelyn ▴ 10
0
votes
1
reply
1.2k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.2 years ago by ★ 3.9k • written 2.2 years ago by • 0
0
votes
3
replies
1.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 90
2
votes
3
replies
1.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 2.4 years ago by 65k • written 2.4 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 2.7 years ago by ★ 6.5k • written 2.7 years ago by • 0
0
votes
1
reply
738
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
2
votes
2
replies
993
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 3.0 years ago by • 0
2
votes
2
replies
2.6k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
3.2 years ago Wuschel ▴ 10
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 11 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
2
votes
0
replies
924
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error topGO go
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
4
votes
1
reply
6.0k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 30
0
votes
0
replies
607
views
ViseaGO merge_enrich_terms ERROR
go
3.8 years ago zaza.inline • 0
0
votes
9
replies
1.6k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.8 years ago camillab. ▴ 10
2
votes
2
replies
865
views
biomart webservice error when using data from Phytozome
software error go
3.9 years ago e.lopez-cortegano • 0
0
votes
1
reply
793
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 10
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
3.9 years ago Ruixuan ▴ 10
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 14 months ago by 65k • written 3.9 years ago by ▴ 30
0
votes
5
replies
1.2k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
3.9 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
896
views
About topGO error
go
updated 4.0 years ago by ▴ 30 • written 4.0 years ago by • 0
2
votes
4
replies
1.4k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
4.0 years ago liz.marjory • 0
0
votes
2
replies
691
views
GO analysis without gene IDs?
deseq2 annotation go
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 60
0
votes
0
replies
597
views
enrichplot pakage no output plot
go
4.0 years ago Hamidreza Hashemi ▴ 20
2
votes
1
reply
5.1k
views
GO of clusterprofiler
go
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO GO
4.0 years ago Al-a ▴ 10
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
6
votes
6
replies
2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
The city by the bay, 4 minutes ago
Colombia, 8 minutes ago
United States, 10 minutes ago
Republic of Ireland, 10 minutes ago
France, 38 minutes ago
Traffic: 715 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6