Showing : go • reset
1
vote
1
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104
views
topGo error loading data
topGO GO
6 weeks ago peter • 0
2
votes
4
replies
329
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 10 weeks ago by • 0
0
votes
1
reply
149
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 3 months ago by ▴ 10 • written 3 months ago by • 0
0
votes
1
reply
190
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 4 months ago by ▴ 540 • written 4 months ago by • 0
0
votes
0
replies
160
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
4 months ago BioinFo.X • 0
0
votes
4
replies
362
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
4 months ago dario.beraldi • 0
2
votes
3
replies
471
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 4 months ago by ▴ 60 • written 4 months ago by ▴ 10
1
vote
3
replies
391
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 7 months ago by 62k • written 7 months ago by ▴ 60
0
votes
13
replies
1.0k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 8 months ago by ★ 3.5k • written 9 months ago by ▴ 10
0
votes
0
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243
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
9 months ago theophile • 0
0
votes
0
replies
1.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
10 months ago Raito92 ▴ 60
15
votes
18
replies
1.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 10 months ago by 47k • written 10 months ago by ▴ 60
0
votes
2
replies
397
views
Gene Onotology: Can't get the goana function to work
edgeR GO
11 months ago Adelyn • 0
0
votes
1
reply
590
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 12 months ago by 3.7k • written 12 months ago by • 0
0
votes
3
replies
853
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 12 months ago by 47k • written 12 months ago by ▴ 70
1
vote
3
replies
870
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 14 months ago by 62k • written 14 months ago by ▴ 10
2
votes
6
replies
695
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 18 months ago by ★ 5.9k • written 18 months ago by • 0
0
votes
1
reply
386
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 20 months ago by 62k • written 20 months ago by • 0
2
votes
2
replies
568
views
retrieve gene IDs from GO.db GO
GO GO.db
21 months ago decppced • 0
0
votes
9
replies
1.0k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 21 months ago by 62k • written 21 months ago by • 0
2
votes
2
replies
1.4k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
23 months ago Wuschel ▴ 10
3
votes
8
replies
2.5k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 months ago by ★ 3.5k • written 2.0 years ago by • 0
2
votes
0
replies
483
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
2.0 years ago Ben ▴ 50
1
vote
1
reply
1.4k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 2.1 years ago by ▴ 10 • written 9.9 years ago by ▴ 340
2
votes
2
replies
596
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 2.2 years ago by 62k • written 2.2 years ago by • 0
2
votes
3
replies
542
views
Error in topGO analysis
software error topGO go
updated 2.4 years ago by 3.7k • written 2.4 years ago by • 0
3
votes
1
reply
2.9k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 2.6 years ago by 62k • written 2.6 years ago by ▴ 20
0
votes
0
replies
348
views
ViseaGO merge_enrich_terms ERROR
go
2.6 years ago zaza.inline • 0
0
votes
9
replies
842
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
2.6 years ago camillab. ▴ 10
2
votes
2
replies
470
views
biomart webservice error when using data from Phytozome
software error go
2.6 years ago e.lopez-cortegano • 0
1
vote
5
replies
605
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
2.7 years ago Ruixuan ▴ 10
0
votes
1
reply
481
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 2.7 years ago by 62k • written 2.7 years ago by ▴ 10
4
votes
8
replies
945
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 6 days ago by 62k • written 2.7 years ago by ▴ 30
0
votes
5
replies
565
views
Error with using getBM function in biomaRt
go r software error R biomaRt
2.7 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
439
views
About topGO error
go
updated 2.8 years ago by ▴ 30 • written 2.8 years ago by • 0
2
votes
4
replies
673
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
2.8 years ago liz.marjory • 0
0
votes
2
replies
312
views
GO analysis without gene IDs?
deseq2 annotation go
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 30
0
votes
0
replies
292
views
enrichplot pakage no output plot
go
2.8 years ago Hamidreza Hashemi ▴ 20
0
votes
1
reply
3.1k
views
GO of clusterprofiler
go
updated 2.8 years ago by 3.7k • written 2.8 years ago by • 0
1
vote
3
replies
860
views
TopGO significant genes
TopGO GO
2.8 years ago Al-a ▴ 10
5
votes
7
replies
985
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 60
6
votes
6
replies
1.1k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 60
0
votes
1
reply
4.4k
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
2.8 years ago tianshenbio • 0
0
votes
0
replies
437
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
2.8 years ago hasse.bossenbroek • 0
0
votes
0
replies
294
views
ViSEAGO, merge_enrich_terms error
go
2.8 years ago m.n • 0
0
votes
4
replies
545
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
2.9 years ago CUCIO199 • 0
2
votes
4
replies
1.1k
views
How to get list of all GOIDs with all genes in each GO term?
go annotation
updated 2.9 years ago by 62k • written 2.9 years ago by • 0
1
vote
3
replies
473
views
Extract the relevant information of the genes sets from the Bioconductor annotation package
org.Rn.eg.db annotation go
updated 2.9 years ago by 62k • written 2.9 years ago by • 0
0
votes
0
replies
267
views
Program to calculate genetic distances with long sequences
probe go
3.0 years ago antoniorevail • 0
0
votes
0
replies
419
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
3.0 years ago info ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons by artem.vorobyev • 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets by nicklesteele532 • 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions? by Hervé Pagès 16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons by swbarnes2 ★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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