Showing : go • reset
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51
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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
0
votes
1
reply
291
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
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 10
0
votes
2
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472
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GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 3 months ago by 66k • written 3 months ago by • 0
0
votes
4
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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 66k • written 8 months ago by • 0
0
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1
reply
639
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 10 months ago by 66k • written 10 months ago by • 0
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0
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469
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
13 months ago Priya • 0
0
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2
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779
views
GO analysis in R vs website
GO RNASeq
14 months ago Nitro • 0
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
1
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1
reply
1.1k
views
topGo error loading data
topGO GO
17 months ago peter • 0
2
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4
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2.2k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 17 months ago by • 0
0
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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
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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
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0
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543
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
19 months ago BioinFo.X • 0
0
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4
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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
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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
1
vote
3
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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
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0
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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
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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
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2
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1.2k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
2.2 years ago Adelyn ▴ 10
0
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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
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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
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1
reply
754
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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
3.0 years ago decppced • 0
0
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9
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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 66k • written 3.1 years ago by • 0
2
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2
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2.7k
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How to download KEGG pathways for list of enriched genes
RNASeqRData GO
3.2 years ago Wuschel ▴ 10
3
votes
11
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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
2
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0
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954
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
2
replies
1.1k
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
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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 66k • written 3.9 years ago by ▴ 30
0
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0
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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
0
votes
1
reply
811
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 3.9 years ago by 66k • written 3.9 years ago by ▴ 10
1
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5
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1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
3.9 years ago Ruixuan ▴ 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 66k • written 4.0 years ago by ▴ 30
0
votes
5
replies
1.2k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
4.0 years ago morteza.aslanzadeh ▴ 30
1
vote
2
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913
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
4.1 years ago liz.marjory • 0
0
votes
2
replies
723
views
GO analysis without gene IDs?
deseq2 annotation go
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 60
0
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0
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613
views
enrichplot pakage no output plot
go
4.1 years ago Hamidreza Hashemi ▴ 20
2
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1
reply
5.3k
views
GO of clusterprofiler
go
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO GO
4.1 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 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
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 66k
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 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
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