Showing : GO • reset
0
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3
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1.3k
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
7 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 15 months ago by • 0
1
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2
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872
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Question on number of genes used in GO analysis
GO clusterProfiler
16 months ago Danté • 0
0
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0
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507
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
19 months ago danalvoronov ▴ 10
4
votes
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 22 months ago by 53k • written 22 months ago by ▴ 10
0
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2
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2.3k
views
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
replies
1.6k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
2.1 years ago Rockbar • 0
1
vote
3
replies
1.5k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 11 months ago by 68k • written 2.2 years ago by • 0
0
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1
reply
1.2k
views
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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856
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.7 years ago Priya • 0
0
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2
replies
1.6k
views
GO analysis in R vs website
GO RNASeq
2.7 years ago Nitro • 0
1
vote
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
views
topGo error loading data
topGO GO
3.0 years ago peter • 0
2
votes
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
reply
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 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
0
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0
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857
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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
replies
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
replies
3.3k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 60
0
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13
replies
4.8k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by ▴ 30
0
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0
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967
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
3.7 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
votes
18
replies
5.2k
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
replies
2.0k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.8 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 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
0
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3
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2.8k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.9 years ago by 53k • written 3.9 years ago by ▴ 90
2
votes
3
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2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
2
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6
replies
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
reply
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
replies
1.6k
views
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
votes
2
replies
3.7k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
4.8 years ago Wuschel ▴ 10
3
votes
11
replies
7.7k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 22 months ago by ★ 4.1k • written 4.9 years ago by • 0
2
votes
0
replies
1.5k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.9 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 12.8 years ago by ▴ 340
2
votes
2
replies
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
votes
3
replies
1.7k
views
Error in topGO analysis
software error topGO go
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
4
votes
1
reply
9.5k
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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846
views
ViseaGO merge_enrich_terms ERROR
go
5.5 years ago zaza.inline • 0
0
votes
9
replies
2.5k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.5 years ago camillab. ▴ 10
2
votes
2
replies
1.4k
views
biomart webservice error when using data from Phytozome
software error go
5.5 years ago e.lopez-cortegano • 0
1
vote
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 2.9 years ago by 68k • written 5.5 years ago by ▴ 30
0
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5
replies
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
Answer: Important: Bioconductor Release 3.22 Delayed by Jasonalker09A • 0
Thanks for @[msn games][1] the update. Connectivity issues can definitely cause a cascade of errors, so delaying the release is completely …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
Awards • All
Popular Question to James W. MacDonald 68k
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