Showing : GO • reset
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
6 months ago • updated 5 months ago GA ▴ 10
7
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9
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1.9k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
1
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2
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829
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Question on number of genes used in GO analysis
GO clusterProfiler
14 months ago Danté • 0
0
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0
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464
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
17 months ago danalvoronov ▴ 10
4
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4
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5.2k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 19 months ago by • 0 • written 7.9 years ago by ▴ 20
1
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3
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2.1k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
19 months ago • updated 13 months ago s.malik • 0
1
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3
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1.5k
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 20 months ago by 53k • written 20 months ago by ▴ 10
0
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2
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2.2k
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 21 months ago by 68k • written 21 months ago by • 0
0
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4
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1.6k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
2.0 years ago Rockbar • 0
1
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3
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1.4k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 9 months ago by 68k • written 2.1 years ago by • 0
0
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1
reply
1.1k
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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0
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834
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.5 years ago Priya • 0
0
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2
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1.5k
views
GO analysis in R vs website
GO RNASeq
2.6 years ago Nitro • 0
1
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4
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2.6k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
2.7 years ago S ▴ 10
1
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1
reply
2.0k
views
topGo error loading data
topGO GO
2.8 years ago peter • 0
2
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4
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3.6k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 2.9 years ago by • 0
0
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1
reply
1.0k
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by • 0
0
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1
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1.1k
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 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
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0
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834
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Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
3.1 years ago BioinFo.X • 0
0
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4
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1.8k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
3.1 years ago dario.beraldi • 0
2
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3
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3.8k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 3.1 years ago by ▴ 150 • written 3.1 years ago by ▴ 10
1
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3
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3.2k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 60
0
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13
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4.6k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 3.4 years ago by ★ 4.1k • written 3.4 years ago by ▴ 30
0
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0
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936
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.5 years ago theophile • 0
0
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0
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4.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.6 years ago Raito92 ▴ 60
15
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18
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5.0k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 60
1
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2
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1.9k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.6 years ago Adelyn ▴ 10
0
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1
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1.9k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
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3
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2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 90
2
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3
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2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 20
2
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6
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2.1k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 4.2 years ago by ★ 6.6k • written 4.2 years ago by • 0
0
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1
reply
1.1k
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
2
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2
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1.5k
views
retrieve gene IDs from GO.db GO
GO GO.db
4.5 years ago decppced • 0
0
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9
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2.5k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
2
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2
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3.7k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
4.7 years ago Wuschel ▴ 10
3
votes
11
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7.5k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 20 months ago by ★ 4.1k • written 4.7 years ago by • 0
2
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0
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1.4k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.7 years ago Ben ▴ 50
2
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1
reply
2.5k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.8 years ago by ▴ 20 • written 12.6 years ago by ▴ 340
2
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2
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1.6k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
2
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3
replies
1.7k
views
Error in topGO analysis
software error topGO go
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
4
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1
reply
9.4k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 40
0
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0
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831
views
ViseaGO merge_enrich_terms ERROR
go
5.3 years ago zaza.inline • 0
0
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9
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2.4k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.3 years ago camillab. ▴ 10
2
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2
replies
1.4k
views
biomart webservice error when using data from Phytozome
software error go
5.4 years ago e.lopez-cortegano • 0
1
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5
replies
1.7k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
5.4 years ago Ruixuan ▴ 10
0
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1
reply
1.2k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 10
4
votes
8
replies
3.3k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.7 years ago by 68k • written 5.4 years ago by ▴ 30
0
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5
replies
2.0k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
5.4 years ago morteza.aslanzadeh ▴ 30
1
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2
replies
1.3k
views
About topGO error
go
updated 5.5 years ago by ▴ 30 • written 5.5 years ago by • 0
2
votes
4
replies
2.1k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
5.5 years ago liz.marjory • 0
1,936 results • Page 1 of 39
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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