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go
•
reset
0
votes
0
replies
130
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
10 weeks ago
danalvoronov
▴ 10
4
votes
4
replies
4.0k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 4 months ago by
jandrade
• 0 • written 6.6 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
1
reply
456
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 4 months ago by
belinda.phipson
▴ 40 • written 4 months ago by
s.malik
• 0
1
vote
3
replies
523
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 5 months ago by
Gordon Smyth
51k • written 5 months ago by
Tyler Sagendorf
▴ 10
0
votes
2
replies
735
views
GO enrichment analysis does not show any pathways in my case
GO
EnrichmentBrowser
updated 5 months ago by
James W. MacDonald
66k • written 6 months ago by
prity6459
• 0
0
votes
4
replies
701
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO
ensembldb
9 months ago
Rockbar
• 0
1
vote
1
reply
557
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 10 months ago by
James W. MacDonald
66k • written 10 months ago by
Alvin
• 0
0
votes
1
reply
718
views
Trouble using biomaRt to pull pathway genes from GO
GO
biomaRt
updated 12 months ago by
James W. MacDonald
66k • written 12 months ago by
cstorer
• 0
0
votes
0
replies
517
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
15 months ago
Priya
• 0
0
votes
2
replies
887
views
GO analysis in R vs website
GO
RNASeq
16 months ago
Nitro
• 0
1
vote
4
replies
1.4k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db
GO
msigdbr
17 months ago
S
▴ 10
1
vote
1
reply
1.3k
views
topGo error loading data
topGO
GO
19 months ago
peter
• 0
2
votes
4
replies
2.4k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 20 months ago by
abhisek001
• 0
0
votes
1
reply
674
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 20 months ago by
Laia
▴ 10 • written 20 months ago by
acram
• 0
0
votes
1
reply
758
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 21 months ago by
Basti
▴ 780 • written 22 months ago by
yeluo
• 0
0
votes
0
replies
601
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO
GeneOntology
LocusIDtogeneIDconversion
22 months ago
BioinFo.X
• 0
0
votes
4
replies
1.2k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
22 months ago
dario.beraldi
• 0
2
votes
3
replies
2.5k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi
GO
clusterProfiler
enrichplot
ensembldb
updated 22 months ago by
merv
▴ 130 • written 22 months ago by
simone.nevills
▴ 10
1
vote
3
replies
2.0k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 2.1 years ago by
James W. MacDonald
66k • written 2.1 years ago by
Raito92
▴ 60
0
votes
13
replies
3.1k
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 2.2 years ago by
Guido Hooiveld
★ 4.0k • written 2.2 years ago by
Lucía
▴ 10
0
votes
0
replies
653
views
What exactly are Nontrivial node in topGO analysis?
topGO
GO
2.3 years ago
theophile
• 0
0
votes
0
replies
3.1k
views
Create a Gene Enrichment GO plot from goana output
goana
RNASeq
edgeR
RnaSeq
GO
2.3 years ago
Raito92
▴ 60
15
votes
18
replies
3.7k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.3 years ago by
Gordon Smyth
51k • written 2.3 years ago by
Raito92
▴ 60
1
vote
2
replies
1.3k
views
Gene Onotology: Can't get the goana function to work
edgeR
GO
2.4 years ago
Adelyn
▴ 10
0
votes
1
reply
1.3k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 2.5 years ago by
Kevin Blighe
★ 4.0k • written 2.5 years ago by
Omurice
• 0
0
votes
3
replies
1.9k
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 2.5 years ago by
Gordon Smyth
51k • written 2.5 years ago by
David R
▴ 90
2
votes
3
replies
1.8k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats
GO
RNASeq
updated 2.7 years ago by
James W. MacDonald
66k • written 2.7 years ago by
joasmile84
▴ 20
2
votes
6
replies
1.5k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO
biomaRt
updated 3.0 years ago by
Mike Smith
★ 6.5k • written 3.0 years ago by
A
• 0
0
votes
1
reply
795
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq
GO
updated 3.2 years ago by
James W. MacDonald
66k • written 3.2 years ago by
Yosapol
• 0
2
votes
2
replies
1.1k
views
retrieve gene IDs from GO.db GO
GO
GO.db
3.2 years ago
decppced
• 0
0
votes
9
replies
1.9k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO
biomartr
annotation
ensemble
fungi
updated 3.2 years ago by
James W. MacDonald
66k • written 3.2 years ago by
Bettina
• 0
2
votes
2
replies
2.9k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
3.4 years ago
Wuschel
▴ 10
3
votes
11
replies
5.4k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 5 months ago by
Guido Hooiveld
★ 4.0k • written 3.5 years ago by
Alberto
• 0
2
votes
0
replies
1.0k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.5 years ago
Ben
▴ 50
2
votes
1
reply
2.0k
views
topGO expected values showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 3.5 years ago by
Doc
▴ 20 • written 11.4 years ago by
Kishor Tappita
▴ 340
2
votes
2
replies
1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.6 years ago by
James W. MacDonald
66k • written 3.6 years ago by
ojong
• 0
2
votes
3
replies
1.2k
views
Error in topGO analysis
software error
topGO
go
updated 3.9 years ago by
Kevin Blighe
★ 4.0k • written 3.9 years ago by
maria.ratto
• 0
4
votes
1
reply
6.5k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 4.1 years ago by
James W. MacDonald
66k • written 4.1 years ago by
adR
▴ 30
0
votes
0
replies
649
views
ViseaGO merge_enrich_terms ERROR
go
4.1 years ago
zaza.inline
• 0
0
votes
9
replies
1.7k
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
4.1 years ago
camillab.
▴ 10
2
votes
2
replies
951
views
biomart webservice error when using data from Phytozome
software error
go
4.1 years ago
e.lopez-cortegano
• 0
1
vote
5
replies
1.2k
views
No enriched GO terms with 1000 more genes
clusterprofiler
GO
4.1 years ago
Ruixuan
▴ 10
0
votes
1
reply
858
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats
GO
R
updated 4.1 years ago by
James W. MacDonald
66k • written 4.1 years ago by
ramonmassoni
▴ 10
4
votes
8
replies
2.4k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 18 months ago by
James W. MacDonald
66k • written 4.2 years ago by
morteza.aslanzadeh
▴ 30
0
votes
5
replies
1.4k
views
Error with using getBM function in biomaRt
go
r
software error
R
biomaRt
4.2 years ago
morteza.aslanzadeh
▴ 30
1
vote
2
replies
967
views
About topGO error
go
updated 4.2 years ago by
abf
▴ 30 • written 4.2 years ago by
iguchi.a0218
• 0
2
votes
4
replies
1.5k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria
GO
KEEG
RNAseq
4.2 years ago
liz.marjory
• 0
0
votes
2
replies
781
views
GO analysis without gene IDs?
deseq2
annotation
go
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
bahmanik@msu.edu
▴ 60
0
votes
0
replies
669
views
enrichplot pakage no output plot
go
4.2 years ago
Hamidreza Hashemi
▴ 20
2
votes
1
reply
5.6k
views
GO of clusterprofiler
go
updated 4.3 years ago by
Kevin Blighe
★ 4.0k • written 4.3 years ago by
doaa.mohamed
• 0
50 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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