Showing : go • reset
0
votes
3
replies
98
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2 days ago by 44k • written 3 days ago by ▴ 70
1
vote
3
replies
231
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 10 weeks ago by 58k • written 10 weeks ago by ▴ 10
2
votes
6
replies
325
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 5 months ago by ★ 5.4k • written 5 months ago by • 0
0
votes
1
reply
182
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 8 months ago by 58k • written 8 months ago by • 0
2
votes
2
replies
295
views
retrieve gene IDs from GO.db GO
GO GO.db
8 months ago decppced • 0
0
votes
9
replies
600
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 8 months ago by 58k • written 9 months ago by • 0
2
votes
2
replies
459
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
11 months ago Wuschel ▴ 10
3
votes
8
replies
995
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 3 months ago by ★ 3.2k • written 12 months ago by • 0
2
votes
0
replies
212
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
12 months ago Ben ▴ 30
0
votes
1
reply
1.1k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 12 months ago by • 0 • written 8.9 years ago by ▴ 340
2
votes
2
replies
354
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 13 months ago by 58k • written 13 months ago by • 0
2
votes
3
replies
318
views
Error in topGO analysis
software error topGO go
updated 17 months ago by 3.4k • written 17 months ago by • 0
2
votes
1
reply
715
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 19 months ago by 58k • written 19 months ago by ▴ 10
0
votes
0
replies
201
views
ViseaGO merge_enrich_terms ERROR
go
19 months ago zaza.inline • 0
0
votes
9
replies
535
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
19 months ago camillab. ▴ 10
2
votes
2
replies
294
views
biomart webservice error when using data from Phytozome
software error go
19 months ago e.lopez-cortegano • 0
1
vote
5
replies
384
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
19 months ago Ruixuan ▴ 10
0
votes
1
reply
247
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 19 months ago by 58k • written 19 months ago by ▴ 10
2
votes
5
replies
510
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
20 months ago morteza.aslanzadeh ▴ 20
0
votes
5
replies
344
views
Error with using getBM function in biomaRt
go r software error R biomaRt
20 months ago morteza.aslanzadeh ▴ 20
1
vote
2
replies
251
views
About topGO error
go
updated 21 months ago by ▴ 30 • written 21 months ago by • 0
2
votes
4
replies
348
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
21 months ago liz.marjory • 0
0
votes
2
replies
185
views
GO analysis without gene IDs?
deseq2 annotation go
updated 21 months ago by 35k • written 21 months ago by ▴ 20
0
votes
0
replies
156
views
enrichplot pakage no output plot
go
21 months ago Hamidreza Hashemi ▴ 20
0
votes
1
reply
1.3k
views
GO of clusterprofiler
go
updated 21 months ago by 3.4k • written 21 months ago by • 0
1
vote
3
replies
246
views
TopGO significant genes
TopGO GO
21 months ago Al-a ▴ 10
4
votes
7
replies
476
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 21 months ago by 44k • written 21 months ago by ▴ 50
6
votes
6
replies
608
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 21 months ago by 44k • written 21 months ago by ▴ 50
0
votes
1
reply
366
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
22 months ago tianshenbio • 0
0
votes
0
replies
215
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
22 months ago hasse.bossenbroek • 0
0
votes
0
replies
158
views
ViSEAGO, merge_enrich_terms error
go
22 months ago m.n • 0
0
votes
4
replies
272
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
22 months ago CUCIO199 • 0
2
votes
4
replies
227
views
How to get list of all GOIDs with all genes in each GO term?
go annotation
updated 22 months ago by 58k • written 22 months ago by • 0
1
vote
3
replies
229
views
Extract the relevant information of the genes sets from the Bioconductor annotation package
org.Rn.eg.db annotation go
updated 22 months ago by 58k • written 22 months ago by • 0
0
votes
0
replies
146
views
Program to calculate genetic distances with long sequences
probe go
23 months ago antoniorevail • 0
0
votes
0
replies
207
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
23 months ago info ▴ 10
0
votes
3
replies
331
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
updated 23 months ago by ★ 2.8k • written 23 months ago by ▴ 20
7
votes
7
replies
500
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
updated 23 months ago by 25k • written 23 months ago by ▴ 20
1
vote
2
replies
220
views
Species, supported by the clusterProfiler package
software error go
updated 24 months ago by 58k • written 24 months ago by • 0
0
votes
2
replies
224
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 2.0 years ago by 58k • written 2.0 years ago by • 0
0
votes
2
replies
220
views
Go terms for Ensemble gene list
go
2.1 years ago Raquel • 0
0
votes
1
reply
940
views
Cannot Install Org.Hs.eg.db package in RStudio
software error annotation go
updated 2.3 years ago by 2.9k • written 2.3 years ago by • 0
2
votes
11
replies
972
views
R gives error when trying to install EnsDb.Hsapiens.v75 package
go
updated 2.3 years ago by 58k • written 2.3 years ago by • 0
1
vote
2
replies
345
views
How could I get index file
go
updated 2.3 years ago by 25k • written 2.3 years ago by • 0
0
votes
1
reply
803
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
2.3 years ago Raito92 ▴ 50
2
votes
1
reply
450
views
biomaRt fails to retrieve GO description for some particular gene
biomart go r bioconductor symbol
2.4 years ago foehn ▴ 80
0
votes
1
reply
352
views
Choosing Gene ontology package
go annotation GOenrichment
updated 2.5 years ago by ▴ 660 • written 2.5 years ago by • 0
0
votes
1
reply
818
views
cnetplot graph independently.
go annotation
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
3
votes
3
replies
446
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 2.6 years ago by 58k • written 2.6 years ago by • 0
4
votes
1
reply
3.8k
views
WGCNA-unable to install GO.db package
go cancer
updated 2.8 years ago by 25k • written 2.8 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
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Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
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Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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