Showing : gene ontology • reset
4
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265
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 9 months ago by 43k • written 9 months ago by ▴ 120
1
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2
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341
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
1
vote
1
reply
200
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Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 11 months ago by 57k • written 11 months ago by ▴ 10
0
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0
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160
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RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
11 months ago ra711 • 0
0
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6
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162
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Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 15 months ago by 57k • written 15 months ago by • 0
0
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3
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190
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GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
updated 16 months ago by ★ 2.7k • written 16 months ago by ▴ 20
7
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7
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280
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GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
updated 16 months ago by 25k • written 16 months ago by ▴ 20
0
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4
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193
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GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 17 months ago by ▴ 300 • written 17 months ago by • 0
1
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2
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296
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Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 20 months ago by ▴ 300 • written 20 months ago by • 0
0
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1
reply
524
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GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
21 months ago Raito92 ▴ 50
3
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1
reply
374
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Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 2.2 years ago by 57k • written 2.2 years ago by • 0
2
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3
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1.3k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
2.7 years ago anton.kratz ▴ 60
3
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3
replies
1.4k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 2.7 years ago by 57k • written 2.7 years ago by ★ 3.0k
1
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1
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476
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News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
2.7 years ago laurent.albou • 0
2
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2
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405
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GO.db source obo file?
gene ontology gostats go.db ontologies
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
0
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0
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310
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How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
3.0 years ago karagozeylul • 0
0
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0
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307
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How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
3.0 years ago karagozeylul • 0
0
votes
1
reply
519
views
Remove highly similar terms from a GO gene set enrichment analysis
clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis
3.0 years ago jan.soderman • 0
1
vote
0
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734
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
3.3 years ago digrigor ▴ 10
0
votes
1
reply
740
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
8
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5
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1.1k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 3.4 years ago by • 0 • written 3.4 years ago by ▴ 60
0
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0
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411
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Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
3.4 years ago jan.soderman • 0
0
votes
1
reply
563
views
Gene ontology enrichment
GO Gene ontology
updated 3.5 years ago by 57k • written 3.5 years ago by ▴ 50
0
votes
1
reply
924
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 3.6 years ago by 57k • written 3.6 years ago by ▴ 10
2
votes
2
replies
1.6k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 3.6 years ago by ★ 1.2k • written 3.6 years ago by • 0
0
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1
reply
656
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topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
3.6 years ago beachboarder900 ▴ 40
0
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2
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2.8k
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No genes found in universe : goana error
edger goana gene ontology
3.7 years ago • updated 3.6 years ago fawazfebin ▴ 30
7
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3
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685
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Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 3.6 years ago by 57k • written 3.6 years ago by ▴ 40
1
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2
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1.8k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 3.7 years ago by 57k • written 3.7 years ago by • 0
0
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4
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585
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discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
gene ontology
3.7 years ago raf4 ▴ 20
1
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2
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695
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Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 3.7 years ago by ★ 1.5k • written 3.7 years ago by • 0
1
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2
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806
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RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
3.8 years ago maeva.mollion • 0
0
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1
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764
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News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 3.9 years ago by 25k • written 3.9 years ago by • 0
3
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5
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848
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Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
3.9 years ago david.rinker ▴ 10
1
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1
reply
577
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Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
software error mygene gene ontology R
updated 3.9 years ago by 57k • written 3.9 years ago by ▴ 10
0
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3
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1.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 4.0 years ago by ▴ 340 • written 4.0 years ago by ▴ 10
2
votes
1
reply
1.4k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 4.0 years ago by ▴ 10 • written 5.2 years ago by ▴ 20
2
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2
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2.6k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 4.1 years ago by ▴ 640 • written 4.1 years ago by ▴ 10
3
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8
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971
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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 4.3 years ago by ★ 6.7k • written 4.3 years ago by • 0
1
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1
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611
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
5
votes
4
replies
716
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 4.4 years ago by ▴ 300 • written 4.4 years ago by ▴ 20
1
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2
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1.2k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 4.4 years ago by ▴ 640 • written 4.7 years ago by ▴ 10
1
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12
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1.6k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 4.5 years ago by ★ 1.2k • written 4.5 years ago by ▴ 10
0
votes
3
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780
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piano runGSA with input from DESEQ2
deseq2 gene ontology piano
4.6 years ago simonp.snoeck • 0
1
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3
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1.2k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 4.7 years ago by ★ 1.2k • written 4.7 years ago by ▴ 10
1
vote
3
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563
views
GoStats ontology count number does not match genes associated with GO term
gostat go terms gene ontology
4.8 years ago adamgetzler • 0
1
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2
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687
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 4.9 years ago by 57k • written 4.9 years ago by • 0
0
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3
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2.0k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 5.1 years ago by ▴ 300 • written 5.1 years ago by ▴ 120
0
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0
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715
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
5.2 years ago mirko • 0
0
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0
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1.1k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
5.3 years ago javier.mendoza • 0
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Comment: how to plot multiple RLEs on same plot? by xiaofeiwang18266 ▴ 20
Thanks a lot!
Answer: Data input for aracne2regulon function in viper package by reef103 • 0
Hi @luna_p , I'm sorry I didn;t see this before. The error might be due to a lack of match between the genes in the network (regulators and…
Comment: deseq2 normalized data with heatmap by Kevin Blighe 3.1k
Hey Ian, specifically just for the heatmap and/or the clustering, we can additionally scale and center the `vsd` or `rld` data. The `scale…
Answer: Difference in mixed test for fry vs mroast by Gordon Smyth 43k
That's a fair question and you're right that the fry/mroast help page doesn't give currently enough information about the mixed p-values. …
Comment: deseq2 normalized data with heatmap by Ian • 0
Hey @kevin , Thanks for the helpful posts! I noticed in your link to this heatmap analysis, you used scale() and not vst(). However, in yo…
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Answer: How does the empirical Bayes moderation (eBayes) in the limma pipeline work?
Differential expression across gene features
C: DESeq on transcripts v/s genes
A: DESeq on transcripts v/s genes
DESeq on transcripts v/s genes
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