Showing : go • reset
0
votes
13
replies
321
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 10 days ago by ★ 3.2k • written 14 days ago by • 0
0
votes
0
replies
79
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
6 weeks ago theophile • 0
0
votes
0
replies
104
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
9 weeks ago Raito92 ▴ 60
15
votes
18
replies
508
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 9 weeks ago by 45k • written 9 weeks ago by ▴ 60
0
votes
2
replies
155
views
Gene Onotology: Can't get the goana function to work
edgeR GO
12 weeks ago Adelyn • 0
0
votes
1
reply
238
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3 months ago by 3.5k • written 3 months ago by • 0
0
votes
3
replies
431
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 4 months ago by 45k • written 4 months ago by ▴ 70
1
vote
3
replies
474
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 6 months ago by 60k • written 6 months ago by ▴ 10
2
votes
6
replies
444
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 9 months ago by ★ 5.6k • written 9 months ago by • 0
0
votes
1
reply
236
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 12 months ago by 60k • written 12 months ago by • 0
2
votes
2
replies
357
views
retrieve gene IDs from GO.db GO
GO GO.db
12 months ago decppced • 0
0
votes
9
replies
724
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 12 months ago by 60k • written 13 months ago by • 0
2
votes
2
replies
734
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
15 months ago Wuschel ▴ 10
3
votes
8
replies
1.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 9 weeks ago by ★ 3.2k • written 16 months ago by • 0
2
votes
0
replies
289
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
16 months ago Ben ▴ 50
2
votes
2
replies
414
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 17 months ago by 60k • written 17 months ago by • 0
2
votes
3
replies
370
views
Error in topGO analysis
software error topGO go
updated 21 months ago by 3.5k • written 21 months ago by • 0
3
votes
1
reply
1.3k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 23 months ago by 60k • written 23 months ago by ▴ 10
0
votes
0
replies
235
views
ViseaGO merge_enrich_terms ERROR
go
23 months ago zaza.inline • 0
0
votes
9
replies
613
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
23 months ago camillab. ▴ 10
2
votes
2
replies
342
views
biomart webservice error when using data from Phytozome
software error go
23 months ago e.lopez-cortegano • 0
0
votes
1
reply
305
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 23 months ago by 60k • written 23 months ago by ▴ 10
1
vote
5
replies
453
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
23 months ago Ruixuan ▴ 10
3
votes
5
replies
622
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
24 months ago morteza.aslanzadeh ▴ 30
0
votes
5
replies
404
views
Error with using getBM function in biomaRt
go r software error R biomaRt
2.0 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
299
views
About topGO error
go
updated 2.1 years ago by ▴ 30 • written 2.1 years ago by • 0
2
votes
4
replies
451
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
2.1 years ago liz.marjory • 0
0
votes
2
replies
216
views
GO analysis without gene IDs?
deseq2 annotation go
updated 2.1 years ago by 37k • written 2.1 years ago by ▴ 30
0
votes
0
replies
195
views
enrichplot pakage no output plot
go
2.1 years ago Hamidreza Hashemi ▴ 20
0
votes
1
reply
2.0k
views
GO of clusterprofiler
go
updated 2.1 years ago by 3.5k • written 2.1 years ago by • 0
1
vote
3
replies
364
views
TopGO significant genes
TopGO GO
2.1 years ago Al-a ▴ 10
4
votes
7
replies
595
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 60
6
votes
6
replies
756
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 60
0
votes
1
reply
577
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
2.1 years ago tianshenbio • 0
0
votes
0
replies
249
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
2.1 years ago hasse.bossenbroek • 0
0
votes
0
replies
192
views
ViSEAGO, merge_enrich_terms error
go
2.1 years ago m.n • 0
0
votes
4
replies
327
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
2.2 years ago CUCIO199 • 0
2
votes
4
replies
316
views
How to get list of all GOIDs with all genes in each GO term?
go annotation
updated 2.2 years ago by 60k • written 2.2 years ago by • 0
1
vote
3
replies
270
views
Extract the relevant information of the genes sets from the Bioconductor annotation package
org.Rn.eg.db annotation go
updated 2.2 years ago by 60k • written 2.2 years ago by • 0
0
votes
0
replies
171
views
Program to calculate genetic distances with long sequences
probe go
2.2 years ago antoniorevail • 0
0
votes
0
replies
269
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
2.3 years ago info ▴ 10
0
votes
3
replies
393
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
updated 2.3 years ago by ★ 2.9k • written 2.3 years ago by ▴ 20
7
votes
7
replies
711
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
updated 2.3 years ago by 25k • written 2.3 years ago by ▴ 20
1
vote
2
replies
277
views
Species, supported by the clusterProfiler package
software error go
updated 2.3 years ago by 60k • written 2.3 years ago by • 0
0
votes
2
replies
271
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 2.3 years ago by 60k • written 2.3 years ago by • 0
0
votes
2
replies
269
views
Go terms for Ensemble gene list
go
2.4 years ago Raquel • 0
0
votes
1
reply
1.1k
views
Cannot Install Org.Hs.eg.db package in RStudio
software error annotation go
updated 2.6 years ago by 3.1k • written 2.6 years ago by • 0
1
vote
2
replies
383
views
How could I get index file
go
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
2
votes
11
replies
1.6k
views
R gives error when trying to install EnsDb.Hsapiens.v75 package
go
updated 2.6 years ago by 60k • written 2.7 years ago by • 0
0
votes
1
reply
933
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
2.7 years ago Raito92 ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
Awards • All
Scholar to Nicole • 0
Teacher to Michael Love 37k
Popular Question to svlachavas ▴ 780
Popular Question to Gordon Smyth 45k
Scholar to Rory Stark ★ 4.4k
Locations • All
Zheng Zhou, 2 minutes ago
San Diego, 3 minutes ago
WEHI, Melbourne, Australia, 7 minutes ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 150 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6