Showing : gene ontology • reset
4
votes
4
replies
357
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 12 months ago by 43k • written 12 months ago by ▴ 120
1
vote
2
replies
483
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 12 months ago by ▴ 10 • written 12 months ago by • 0
1
vote
1
reply
265
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 14 months ago by 58k • written 14 months ago by ▴ 10
0
votes
0
replies
214
views
RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
14 months ago ra711 • 0
0
votes
6
replies
235
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 18 months ago by 58k • written 18 months ago by • 0
0
votes
3
replies
249
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
updated 19 months ago by ★ 2.7k • written 19 months ago by ▴ 20
7
votes
7
replies
370
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
updated 19 months ago by 25k • written 19 months ago by ▴ 20
0
votes
4
replies
257
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 20 months ago by ▴ 300 • written 20 months ago by • 0
1
vote
2
replies
393
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 23 months ago by ▴ 300 • written 23 months ago by • 0
0
votes
1
reply
624
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
24 months ago Raito92 ▴ 50
3
votes
1
reply
422
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 2.4 years ago by 58k • written 2.4 years ago by • 0
2
votes
3
replies
1.5k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
2.9 years ago anton.kratz ▴ 60
3
votes
3
replies
1.5k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 3.0 years ago by 58k • written 3.0 years ago by ★ 3.0k
1
vote
1
reply
523
views
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
3.0 years ago laurent.albou • 0
2
votes
2
replies
471
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 3.1 years ago by 25k • written 3.1 years ago by • 0
0
votes
0
replies
342
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
3.2 years ago karagozeylul • 0
0
votes
0
replies
338
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
3.2 years ago karagozeylul • 0
0
votes
1
reply
567
views
Remove highly similar terms from a GO gene set enrichment analysis
clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis
3.3 years ago jan.soderman • 0
1
vote
0
replies
827
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
3.5 years ago digrigor ▴ 10
0
votes
1
reply
789
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
8
votes
5
replies
1.2k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 60
0
votes
0
replies
444
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
3.7 years ago jan.soderman • 0
0
votes
1
reply
594
views
Gene ontology enrichment
GO Gene ontology
updated 3.7 years ago by 58k • written 3.7 years ago by ▴ 50
0
votes
1
reply
972
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 3.8 years ago by 58k • written 3.8 years ago by ▴ 10
2
votes
2
replies
1.7k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 3.8 years ago by ★ 1.2k • written 3.9 years ago by • 0
0
votes
1
reply
693
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
3.9 years ago beachboarder900 ▴ 40
0
votes
2
replies
2.9k
views
No genes found in universe : goana error
edger goana gene ontology
4.0 years ago • updated 3.9 years ago fawazfebin ▴ 30
7
votes
3
replies
746
views
Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 3.9 years ago by 58k • written 3.9 years ago by ▴ 40
1
vote
2
replies
1.9k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 3.9 years ago by 58k • written 3.9 years ago by • 0
0
votes
4
replies
673
views
discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
gene ontology
4.0 years ago • updated 3.9 years ago raf4 ▴ 20
1
vote
2
replies
770
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 4.0 years ago by ★ 1.5k • written 4.0 years ago by • 0
1
vote
2
replies
885
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
4.0 years ago maeva.mollion • 0
0
votes
1
reply
799
views
News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
3
votes
5
replies
896
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
4.2 years ago david.rinker ▴ 10
1
vote
1
reply
615
views
Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
software error mygene gene ontology R
updated 4.2 years ago by 58k • written 4.2 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 4.2 years ago by ▴ 340 • written 4.3 years ago by ▴ 10
2
votes
1
reply
1.5k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 4.2 years ago by ▴ 10 • written 5.5 years ago by ▴ 20
2
votes
2
replies
2.8k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 4.4 years ago by ▴ 650 • written 4.4 years ago by ▴ 10
3
votes
8
replies
1.0k
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 4.5 years ago by ★ 6.7k • written 4.5 years ago by • 0
1
vote
1
reply
644
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
5
votes
4
replies
763
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 4.7 years ago by ▴ 300 • written 4.7 years ago by ▴ 20
1
vote
2
replies
1.3k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 4.7 years ago by ▴ 650 • written 5.0 years ago by ▴ 10
1
vote
12
replies
1.7k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 4.8 years ago by ★ 1.2k • written 4.8 years ago by ▴ 10
0
votes
3
replies
923
views
piano runGSA with input from DESEQ2
deseq2 gene ontology piano
4.9 years ago simonp.snoeck • 0
1
vote
3
replies
1.2k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 5.0 years ago by ★ 1.2k • written 5.0 years ago by ▴ 10
1
vote
3
replies
595
views
GoStats ontology count number does not match genes associated with GO term
gostat go terms gene ontology
5.0 years ago adamgetzler • 0
1
vote
2
replies
729
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 5.1 years ago by 58k • written 5.1 years ago by • 0
0
votes
3
replies
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 5.3 years ago by ▴ 300 • written 5.3 years ago by ▴ 120
0
votes
0
replies
753
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
5.4 years ago mirko • 0
0
votes
0
replies
1.1k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
5.6 years ago javier.mendoza • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Reading vcf file with readVcf by James W. MacDonald 58k
Usually when you run out of RAM, you usually get an error saying that 'R couldn't allocate a vector of size <some number>'. When it just sa…
Answer: Genic annotations of whole hg38 by James W. MacDonald 58k
What exactly do you mean by 'proportion of genic annotations'? One possibility would be to see what proportion of all the exons are covered…
Answer: Understanding output of Negative Binomial in DESeq2 by Michael Love 34k
> Does this mean that there are seven genes in total that will have significant adjusted p-value? yes > i recall when multiple linea…
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
The above sounds fine to me. I do not recommend adding 1 to all expected counts for DESeq2. It is strange that every gene contains a …
Answer: Swish direction of comparison based on order of factors by Michael Love 34k
hi Jean, Thanks for the question, this wasn't explicitly stated in the documentation, so I've updated it, here are the new sections in m…
Votes
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Answer: Effect size using likelihood ratio test in DESeq2
Comment: ggtree install
Awards • All
Scholar to Gordon Smyth 43k
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Hans-Ulrich Klein ▴ 330
Popular Question to Hervé Pagès 15k
Scholar to Jiang, Mike ★ 1.3k
Locations • All
WEHI, Melbourne, Australia, 13 minutes ago
Pakistan, 16 minutes ago
CRUK, Cambridge, UK, 21 minutes ago
San Diego, 23 minutes ago
United States, 52 minutes ago
Traffic: 348 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6