Showing : gene ontology • reset
4
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4
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1.6k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 4.3 years ago by 52k • written 4.3 years ago by ▴ 120
2
votes
2
replies
2.2k
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 4.3 years ago by ▴ 50 • written 4.3 years ago by • 0
1
vote
1
reply
1.3k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 4.4 years ago by 67k • written 4.4 years ago by ▴ 10
0
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0
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945
views
RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
4.4 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 20 months ago by ▴ 50 • written 4.8 years ago by ▴ 20
3
votes
4
replies
2.2k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.8 years ago • updated 21 months ago samwhite ▴ 20
7
votes
9
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4.1k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.8 years ago • updated 21 months ago samwhite ▴ 20
0
votes
4
replies
1.3k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 4.9 years ago by ▴ 350 • written 4.9 years ago by • 0
1
vote
2
replies
1.5k
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 5.2 years ago by ▴ 350 • written 5.2 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
5.2 years ago Raito92 ▴ 60
3
votes
1
reply
1.2k
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 5.6 years ago by 67k • written 5.6 years ago by • 0
2
votes
3
replies
5.2k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
6.2 years ago anton.kratz ▴ 60
3
votes
3
replies
4.1k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 6.2 years ago by 67k • written 6.2 years ago by ★ 4.1k
1
vote
1
reply
1.3k
views
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
6.2 years ago laurent.albou • 0
2
votes
2
replies
1.6k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
votes
0
replies
842
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
6.5 years ago karagozeylul • 0
0
votes
0
replies
881
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
6.5 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
6.5 years ago jan.soderman • 0
1
vote
0
replies
2.4k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.8 years ago digrigor ▴ 10
0
votes
1
reply
1.9k
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 6.8 years ago by 52k • written 6.9 years ago by • 0
8
votes
5
replies
2.7k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
6.9 years ago jan.soderman • 0
0
votes
1
reply
1.0k
views
Gene ontology enrichment
GO Gene ontology
updated 7.0 years ago by 67k • written 7.0 years ago by ▴ 50
0
votes
1
reply
1.9k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 7.0 years ago by 67k • written 7.0 years ago by ▴ 10
2
votes
2
replies
4.0k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by ▴ 20
0
votes
1
reply
1.3k
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
7.1 years ago beachboarder900 ▴ 40
3
votes
2
replies
5.0k
views
No genes found in universe : goana error
edger goana gene ontology
7.2 years ago • updated 7.1 years ago fawazfebin ▴ 60
7
votes
3
replies
1.7k
views
Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 7.1 years ago by 67k • written 7.1 years ago by ▴ 40
1
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2
replies
3.2k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 7.1 years ago by 67k • written 7.2 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
7.2 years ago raf4 ▴ 30
1
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2
replies
2.5k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by • 0
1
vote
2
replies
2.4k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.3 years ago maeva.mollion • 0
0
votes
1
reply
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 7.4 years ago by 25k • written 7.4 years ago by • 0
3
votes
5
replies
1.9k
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
7.4 years ago david.rinker ▴ 10
1
vote
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 7.4 years ago by 67k • written 7.4 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 7.4 years ago by ▴ 370 • written 7.5 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 7.5 years ago by ▴ 10 • written 8.7 years ago by ▴ 20
2
votes
2
replies
4.8k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 7.6 years ago by ▴ 760 • written 7.6 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 7.8 years ago by ★ 6.8k • written 7.8 years ago by • 0
1
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1
reply
1.3k
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 7.8 years ago by 52k • written 7.8 years ago by • 0
5
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4
replies
1.8k
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 7.9 years ago by ▴ 350 • written 7.9 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 7.9 years ago by ▴ 760 • written 8.2 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 8.0 years ago by ★ 1.2k • written 8.0 years ago by ▴ 10
0
votes
3
replies
2.0k
views
piano runGSA with input from DESEQ2
deseq2 gene ontology piano
8.1 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 8.2 years ago by ★ 1.2k • written 8.2 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
8.3 years ago adamgetzler • 0
1
vote
2
replies
1.6k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 8.4 years ago by 67k • written 8.4 years ago by • 0
0
votes
3
replies
4.1k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 8.6 years ago by ▴ 350 • written 8.6 years ago by ▴ 130
0
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0
replies
1.5k
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
8.7 years ago mirko • 0
0
votes
0
replies
1.6k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
8.8 years ago javier.mendoza • 0
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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