Showing : Gene ontology • reset
4
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1.6k
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 4.4 years ago by 52k • written 4.4 years ago by ▴ 120
2
votes
2
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2.3k
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 4.4 years ago by ▴ 50 • written 4.4 years ago by • 0
1
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1
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1.4k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 10
0
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0
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964
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RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
4.5 years ago ra711 • 0
5
votes
7
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2.3k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 21 months ago by ▴ 50 • written 4.9 years ago by ▴ 20
3
votes
4
replies
2.3k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.9 years ago • updated 23 months ago samwhite ▴ 20
7
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9
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4.3k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.9 years ago • updated 22 months ago samwhite ▴ 20
0
votes
4
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1.3k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.0 years ago by ▴ 350 • written 5.0 years ago by • 0
1
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2
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1.5k
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Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 5.3 years ago by ▴ 350 • written 5.3 years ago by • 0
0
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1
reply
2.5k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
5.4 years ago Raito92 ▴ 60
3
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1
reply
1.3k
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
2
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3
replies
5.3k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
6.3 years ago anton.kratz ▴ 60
3
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3
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4.2k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 6.3 years ago by 67k • written 6.3 years ago by ★ 4.1k
1
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1
reply
1.4k
views
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
6.3 years ago laurent.albou • 0
2
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2
replies
1.6k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
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0
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857
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
6.6 years ago karagozeylul • 0
0
votes
0
replies
909
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
6.6 years ago karagozeylul • 0
0
votes
1
reply
1.6k
views
Remove highly similar terms from a GO gene set enrichment analysis
clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis
6.6 years ago jan.soderman • 0
1
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0
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2.5k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.9 years ago digrigor ▴ 10
0
votes
1
reply
1.9k
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
8
votes
5
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2.7k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 60
0
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0
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1.2k
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
7.0 years ago jan.soderman • 0
0
votes
1
reply
1.1k
views
Gene ontology enrichment
GO Gene ontology
updated 7.1 years ago by 67k • written 7.1 years ago by ▴ 50
0
votes
1
reply
1.9k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 7.2 years ago by 67k • written 7.2 years ago by ▴ 10
2
votes
2
replies
4.1k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by ▴ 20
0
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1
reply
1.3k
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
7.2 years ago beachboarder900 ▴ 40
3
votes
2
replies
5.0k
views
No genes found in universe : goana error
edger goana gene ontology
7.3 years ago • updated 7.2 years ago fawazfebin ▴ 60
7
votes
3
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1.7k
views
Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 7.2 years ago by 67k • written 7.2 years ago by ▴ 40
1
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2
replies
3.3k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 7.3 years ago by 67k • written 7.3 years ago by • 0
0
votes
4
replies
1.4k
views
discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
gene ontology
7.3 years ago raf4 ▴ 30
1
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2
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2.6k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
1
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2
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2.5k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.4 years ago maeva.mollion • 0
0
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1
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1.4k
views
News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 7.5 years ago by 25k • written 7.5 years ago by • 0
3
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5
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2.0k
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
7.5 years ago david.rinker ▴ 10
1
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1
reply
1.3k
views
Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
software error mygene gene ontology R
updated 7.5 years ago by 67k • written 7.5 years ago by ▴ 10
0
votes
3
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2.5k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 7.6 years ago by ▴ 370 • written 7.6 years ago by ▴ 10
2
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1
reply
2.4k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 7.6 years ago by ▴ 10 • written 8.8 years ago by ▴ 20
2
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2
replies
4.8k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 7.7 years ago by ▴ 760 • written 7.7 years ago by ▴ 10
3
votes
8
replies
2.4k
views
How does the org.Dm.eg.db package deal with NOT annotation qualifiers when annotating genes to GO?
org.dm.eg.db gene ontology go enrichment annotation NOT
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by • 0
1
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1
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1.4k
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 7.9 years ago by 52k • written 7.9 years ago by • 0
5
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4
replies
1.9k
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 8.0 years ago by ▴ 350 • written 8.0 years ago by ▴ 20
1
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2
replies
2.9k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 8.0 years ago by ▴ 760 • written 8.3 years ago by ▴ 10
1
vote
12
replies
3.9k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 8.1 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
0
votes
3
replies
2.0k
views
piano runGSA with input from DESEQ2
deseq2 gene ontology piano
8.2 years ago simonp.snoeck • 0
1
vote
3
replies
2.6k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 10
1
vote
3
replies
1.2k
views
GoStats ontology count number does not match genes associated with GO term
gostat go terms gene ontology
8.4 years ago adamgetzler • 0
1
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2
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1.7k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 8.5 years ago by 67k • written 8.5 years ago by • 0
0
votes
3
replies
4.2k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 8.7 years ago by ▴ 350 • written 8.7 years ago by ▴ 130
0
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0
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1.5k
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
8.8 years ago mirko • 0
0
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0
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1.6k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
8.9 years ago javier.mendoza • 0
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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