Showing : GO • reset
7
votes
9
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1.4k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
2
replies
527
views
Question on number of genes used in GO analysis
GO clusterProfiler
6 months ago Danté • 0
0
votes
0
replies
308
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
9 months ago danalvoronov ▴ 10
4
votes
4
replies
4.6k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 11 months ago by • 0 • written 7.2 years ago by ▴ 20
1
vote
3
replies
1.7k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
12 months ago • updated 5 months ago s.malik • 0
1
vote
3
replies
1.0k
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 months ago by 52k • written 12 months ago by ▴ 10
0
votes
2
replies
1.6k
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
4
replies
1.2k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
16 months ago Rockbar • 0
1
vote
3
replies
1.0k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 7 weeks ago by 68k • written 17 months ago by • 0
0
votes
1
reply
912
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
671
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
22 months ago Priya • 0
0
votes
2
replies
1.2k
views
GO analysis in R vs website
GO RNASeq
23 months ago Nitro • 0
1
vote
4
replies
1.9k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
2.0 years ago S ▴ 10
1
vote
1
reply
1.7k
views
topGo error loading data
topGO GO
2.2 years ago peter • 0
2
votes
4
replies
3.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 2.3 years ago by • 0
0
votes
1
reply
851
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 2.3 years ago by ▴ 10 • written 2.3 years ago by • 0
0
votes
1
reply
931
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 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
votes
0
replies
732
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
2.4 years ago BioinFo.X • 0
0
votes
4
replies
1.5k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
2.4 years ago dario.beraldi • 0
2
votes
3
replies
3.3k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.4 years ago by ▴ 150 • written 2.4 years ago by ▴ 10
1
vote
3
replies
2.7k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 60
0
votes
13
replies
3.9k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 2.8 years ago by ★ 4.1k • written 2.8 years ago by ▴ 30
0
votes
0
replies
786
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
2.9 years ago theophile • 0
0
votes
0
replies
3.8k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
2.9 years ago Raito92 ▴ 60
15
votes
18
replies
4.4k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 2.9 years ago by 52k • written 2.9 years ago by ▴ 60
1
vote
2
replies
1.7k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.0 years ago Adelyn ▴ 10
0
votes
1
reply
1.7k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
3
replies
2.3k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.1 years ago by 52k • written 3.1 years ago by ▴ 90
2
votes
3
replies
2.2k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 20
2
votes
6
replies
1.8k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 3.6 years ago by ★ 6.6k • written 3.6 years ago by • 0
0
votes
1
reply
963
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
2
votes
2
replies
1.3k
views
retrieve gene IDs from GO.db GO
GO GO.db
3.8 years ago decppced • 0
0
votes
9
replies
2.2k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
2
votes
2
replies
3.3k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
4.0 years ago Wuschel ▴ 10
3
votes
11
replies
6.5k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 13 months ago by ★ 4.1k • written 4.1 years ago by • 0
2
votes
0
replies
1.2k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.1 years ago Ben ▴ 50
2
votes
1
reply
2.2k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.1 years ago by ▴ 20 • written 12.0 years ago by ▴ 340
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
2
votes
3
replies
1.4k
views
Error in topGO analysis
software error topGO go
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
4
votes
1
reply
8.3k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 40
0
votes
0
replies
740
views
ViseaGO merge_enrich_terms ERROR
go
4.7 years ago zaza.inline • 0
0
votes
9
replies
2.1k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.7 years ago camillab. ▴ 10
2
votes
2
replies
1.3k
views
biomart webservice error when using data from Phytozome
software error go
4.7 years ago e.lopez-cortegano • 0
1
vote
5
replies
1.5k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
4.7 years ago Ruixuan ▴ 10
0
votes
1
reply
1.0k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 10
4
votes
8
replies
2.9k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.1 years ago by 68k • written 4.8 years ago by ▴ 30
0
votes
5
replies
1.7k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
4.8 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
1.1k
views
About topGO error
go
updated 4.8 years ago by ▴ 30 • written 4.8 years ago by • 0
2
votes
4
replies
1.8k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
4.8 years ago liz.marjory • 0
0
votes
2
replies
933
views
GO analysis without gene IDs?
deseq2 annotation go
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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