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go
•
reset
1
vote
1
reply
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
abhisek001
• 0
0
votes
1
reply
149
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 3 months ago by
Laia
▴ 10 • written 3 months ago by
acram
• 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
Basti
▴ 540 • written 4 months ago by
yeluo
• 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
merv
▴ 60 • written 4 months ago by
simone.nevills
▴ 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
James W. MacDonald
62k • written 7 months ago by
Raito92
▴ 60
0
votes
13
replies
1.0k
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 8 months ago by
Guido Hooiveld
★ 3.5k • written 9 months ago by
Lucía
▴ 10
0
votes
0
replies
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
Gordon Smyth
47k • written 10 months ago by
Raito92
▴ 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
Kevin Blighe
3.7k • written 12 months ago by
Omurice
• 0
0
votes
3
replies
853
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 12 months ago by
Gordon Smyth
47k • written 12 months ago by
David R
▴ 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
James W. MacDonald
62k • written 14 months ago by
joasmile84
▴ 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
Mike Smith
★ 5.9k • written 18 months ago by
A
• 0
0
votes
1
reply
386
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq
GO
updated 20 months ago by
James W. MacDonald
62k • written 20 months ago by
Yosapol
• 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
James W. MacDonald
62k • written 21 months ago by
Bettina
• 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
Guido Hooiveld
★ 3.5k • written 2.0 years ago by
Alberto
• 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
Doc
▴ 10 • written 9.9 years ago by
Kishor Tappita
▴ 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
James W. MacDonald
62k • written 2.2 years ago by
ojong
• 0
2
votes
3
replies
542
views
Error in topGO analysis
software error
topGO
go
updated 2.4 years ago by
Kevin Blighe
3.7k • written 2.4 years ago by
maria.ratto
• 0
3
votes
1
reply
2.9k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 2.6 years ago by
James W. MacDonald
62k • written 2.6 years ago by
adR
▴ 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
James W. MacDonald
62k • written 2.7 years ago by
ramonmassoni
▴ 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
James W. MacDonald
62k • written 2.7 years ago by
morteza.aslanzadeh
▴ 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
abf
▴ 30 • written 2.8 years ago by
iguchi.a0218
• 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
Michael Love
39k • written 2.8 years ago by
bahmanik@msu.edu
▴ 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
Kevin Blighe
3.7k • written 2.8 years ago by
doaa.mohamed
• 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
Gordon Smyth
47k • written 2.8 years ago by
Raito92
▴ 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
Gordon Smyth
47k • written 2.8 years ago by
Raito92
▴ 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
James W. MacDonald
62k • written 2.9 years ago by
theodore.killian
• 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
James W. MacDonald
62k • written 2.9 years ago by
jose.wo
• 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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