Showing : go • reset
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 5 weeks ago by • 0 • written 6.4 years ago by ▴ 20
0
votes
1
reply
247
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 8 weeks ago by ▴ 40 • written 8 weeks ago by • 0
1
vote
3
replies
337
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 10
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 12 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
2
replies
388
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 3 months ago by 65k • written 3 months ago by • 0
0
votes
4
replies
549
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago Rockbar • 0
1
vote
1
reply
419
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
1
reply
612
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
453
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
8.9k
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
updated 12 months ago by • 0 • written 4.1 years ago by • 0
7
votes
9
replies
3.0k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.2 years ago • updated 13 months ago samwhite ▴ 20
0
votes
2
replies
2.6k
views
Using biomaRt for getting Go Terms
GO biomaRt GO biomaRt
updated 13 months ago by • 0 • written 13.3 years ago by ▴ 190
0
votes
2
replies
743
views
GO analysis in R vs website
GO RNASeq
13 months ago Nitro • 0
3
votes
4
replies
1.5k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.2 years ago • updated 13 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
14 months ago S ▴ 10
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 15 months ago by 65k • written 3.9 years ago by ▴ 30
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
597
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
680
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
votes
0
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519
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
19 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
0
votes
3
replies
4.8k
views
how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 22 months ago by • 0 • written 12.2 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 11.7 years ago by ▴ 70
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
1
reply
2.0k
views
Registration Confirmation
GO GO
updated 2.0 years ago by • 0 • written 14.4 years ago by ▴ 10
0
votes
0
replies
583
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
3.4k
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
2.2 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 2.3 years ago by 50k • written 2.3 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
744
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
998
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
2
votes
0
replies
930
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 3.3 years ago by ▴ 20 • written 11.1 years ago by ▴ 340
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 3.7 years ago by ★ 3.9k • written 3.7 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
608
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
3.9 years ago camillab. ▴ 10
2
votes
2
replies
871
views
biomart webservice error when using data from Phytozome
software error go
3.9 years ago e.lopez-cortegano • 0
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
3.9 years ago Ruixuan ▴ 10
0
votes
1
reply
802
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
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Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
Votes
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
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