Showing : gene ontology • reset
4
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4
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640
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 23 months ago by 46k • written 23 months ago by ▴ 120
1
vote
2
replies
858
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 23 months ago by ▴ 40 • written 23 months ago by • 0
1
vote
1
reply
520
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 2.1 years ago by 60k • written 2.1 years ago by ▴ 10
0
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0
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367
views
RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
2.1 years ago ra711 • 0
0
votes
6
replies
429
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 2.4 years ago by 60k • written 2.4 years ago by • 0
0
votes
3
replies
435
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
updated 2.5 years ago by ★ 2.9k • written 2.5 years ago by ▴ 20
7
votes
7
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835
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
updated 2.5 years ago by 25k • written 2.5 years ago by ▴ 20
0
votes
4
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442
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 2.5 years ago by ▴ 300 • written 2.5 years ago by • 0
1
vote
2
replies
607
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 2.8 years ago by ▴ 300 • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
2.9 years ago Raito92 ▴ 60
3
votes
1
reply
631
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 3.3 years ago by 60k • written 3.3 years ago by • 0
2
votes
3
replies
2.3k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
3.8 years ago anton.kratz ▴ 60
3
votes
3
replies
2.3k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 3.9 years ago by 60k • written 3.9 years ago by ★ 3.3k
1
vote
1
reply
689
views
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
3.9 years ago laurent.albou • 0
2
votes
2
replies
723
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 4.0 years ago by 25k • written 4.0 years ago by • 0
0
votes
0
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407
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
4.1 years ago karagozeylul • 0
0
votes
0
replies
415
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
4.1 years ago karagozeylul • 0
0
votes
1
reply
714
views
Remove highly similar terms from a GO gene set enrichment analysis
clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis
4.2 years ago jan.soderman • 0
1
vote
0
replies
1.2k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
4.4 years ago digrigor ▴ 10
0
votes
1
reply
1.0k
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 4.5 years ago by 46k • written 4.5 years ago by • 0
8
votes
5
replies
1.5k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 4.5 years ago by • 0 • written 4.5 years ago by ▴ 60
0
votes
0
replies
541
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
4.5 years ago jan.soderman • 0
0
votes
1
reply
699
views
Gene ontology enrichment
GO Gene ontology
updated 4.6 years ago by 60k • written 4.6 years ago by ▴ 50
0
votes
1
reply
1.1k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 4.7 years ago by 60k • written 4.7 years ago by ▴ 10
2
votes
2
replies
2.2k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 4.7 years ago by ★ 1.2k • written 4.7 years ago by • 0
0
votes
1
reply
790
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
4.7 years ago beachboarder900 ▴ 40
3
votes
2
replies
3.4k
views
No genes found in universe : goana error
edger goana gene ontology
4.8 years ago fawazfebin ▴ 50
7
votes
3
replies
902
views
Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 4.8 years ago by 60k • written 4.8 years ago by ▴ 40
1
vote
2
replies
2.2k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 4.8 years ago by 60k • written 4.8 years ago by • 0
0
votes
4
replies
836
views
discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
gene ontology
4.8 years ago raf4 ▴ 20
1
vote
2
replies
1.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 4.9 years ago by ★ 1.5k • written 4.9 years ago by • 0
1
vote
2
replies
1.2k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
4.9 years ago maeva.mollion • 0
0
votes
1
reply
905
views
News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
3
votes
5
replies
1.1k
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
5.1 years ago david.rinker ▴ 10
1
vote
1
reply
752
views
Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
software error mygene gene ontology R
updated 5.1 years ago by 60k • written 5.1 years ago by ▴ 10
0
votes
3
replies
1.6k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 5.1 years ago by ▴ 360 • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.7k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 5.1 years ago by ▴ 10 • written 6.4 years ago by ▴ 20
2
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2
replies
3.3k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 5.3 years ago by ▴ 690 • written 5.3 years ago by ▴ 10
3
votes
8
replies
1.3k
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 5.4 years ago by ★ 6.7k • written 5.4 years ago by • 0
1
vote
1
reply
776
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 5.5 years ago by 46k • written 5.5 years ago by • 0
5
votes
4
replies
899
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 5.6 years ago by ▴ 300 • written 5.6 years ago by ▴ 20
1
vote
2
replies
1.6k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 5.6 years ago by ▴ 690 • written 5.9 years ago by ▴ 10
1
vote
12
replies
2.0k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by ▴ 10
0
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3
replies
1.1k
views
piano runGSA with input from DESEQ2
deseq2 gene ontology piano
5.8 years ago simonp.snoeck • 0
1
vote
3
replies
1.4k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by ▴ 10
1
vote
3
replies
685
views
GoStats ontology count number does not match genes associated with GO term
gostat go terms gene ontology
5.9 years ago adamgetzler • 0
1
vote
2
replies
857
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 6.0 years ago by 60k • written 6.0 years ago by • 0
0
votes
3
replies
2.6k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 6.2 years ago by ▴ 300 • written 6.2 years ago by ▴ 120
0
votes
0
replies
882
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
6.3 years ago mirko • 0
0
votes
0
replies
1.2k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
6.4 years ago javier.mendoza • 0
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Comment: unable to install.packages("spatialLIBD") by Leonardo Collado Torres ▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment by Martin Morgan 25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Delta._.43 ▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Alejandro Reyes ★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Answer: spot- vs cell-level data access by Leonardo Collado Torres ▴ 1000
Hi, The `SingleCellExperiment` object you can download with `fetch_data(type = "sce")` pre-dates the creation of `SpatialExperiment`. No…
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Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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