Showing : gene ontology • reset
4
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4
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2.0k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 120
2
votes
2
replies
2.7k
views
clusterporfiler enrichGO plot
clusterprofiler gene ontology plot
updated 5.1 years ago by ▴ 50 • written 5.1 years ago by • 0
1
vote
1
reply
1.6k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
0
votes
0
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1.1k
views
RDAVIDWebService Package Official Gene Symbol IDs in GO Term Tables
RDAVIDWebService Gene Ontology GOTerm biomaRt
5.3 years ago ra711 • 0
5
votes
7
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2.8k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 2.5 years ago by ▴ 50 • written 5.6 years ago by ▴ 20
3
votes
4
replies
2.9k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
5.7 years ago • updated 2.6 years ago samwhite ▴ 20
7
votes
9
replies
5.3k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
5.7 years ago • updated 2.6 years ago samwhite ▴ 20
0
votes
4
replies
1.6k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.8 years ago by ▴ 350 • written 5.8 years ago by • 0
1
vote
2
replies
1.8k
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress heatmap gene ontology plot
updated 6.1 years ago by ▴ 350 • written 6.1 years ago by • 0
0
votes
1
reply
2.8k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
6.1 years ago Raito92 ▴ 60
3
votes
1
reply
1.4k
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
2
votes
3
replies
5.8k
views
No gene set have size > 10 ...
clusterprofiler gene ontology
7.0 years ago anton.kratz ▴ 60
3
votes
3
replies
4.6k
views
how to find ensembl genes belonging to a GO category?
biomart gene ontology GO
updated 7.1 years ago by 68k • written 7.1 years ago by ★ 4.1k
1
vote
1
reply
1.5k
views
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
gene ontology go ontology bioinformatics genomics News
7.1 years ago laurent.albou • 0
2
votes
2
replies
1.9k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
0
votes
0
replies
1.1k
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
7.3 years ago karagozeylul • 0
0
votes
0
replies
1.1k
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
7.3 years ago karagozeylul • 0
0
votes
1
reply
1.9k
views
Remove highly similar terms from a GO gene set enrichment analysis
clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis
7.4 years ago jan.soderman • 0
1
vote
0
replies
2.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.6 years ago digrigor ▴ 10
0
votes
1
reply
2.1k
views
[goana] function within edgeR not working for Arabidopsis
gene ontology
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
8
votes
5
replies
3.0k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 60
0
votes
0
replies
1.4k
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries gene ontology enrichment analysis
7.8 years ago jan.soderman • 0
0
votes
1
reply
1.2k
views
Gene ontology enrichment
GO Gene ontology
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 50
0
votes
1
reply
2.2k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 10
2
votes
2
replies
4.6k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 8.0 years ago by ★ 1.2k • written 8.0 years ago by ▴ 20
0
votes
1
reply
1.5k
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology topGO GO
8.0 years ago beachboarder900 ▴ 40
3
votes
2
replies
5.3k
views
No genes found in universe : goana error
edger goana gene ontology
8.1 years ago • updated 8.0 years ago fawazfebin ▴ 60
7
votes
3
replies
2.0k
views
Presence of GO annotations for human mitochondrial genes in org.Hs.eg.db?
org.hs.eg.db gene ontology mitochondria
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 40
1
vote
2
replies
3.5k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
0
votes
4
replies
1.6k
views
discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
gene ontology
8.1 years ago • updated 8.0 years ago raf4 ▴ 30
1
vote
2
replies
3.0k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by • 0
1
vote
2
replies
2.8k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
8.1 years ago maeva.mollion • 0
0
votes
1
reply
1.5k
views
News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 8.2 years ago by 25k • written 8.2 years ago by • 0
3
votes
5
replies
2.2k
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
8.3 years ago david.rinker ▴ 10
1
vote
1
reply
1.6k
views
Returning gene functional annotations with gene symbols as input (using mygene Bioconductor package)
software error mygene gene ontology R
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 10
0
votes
3
replies
2.8k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 8.3 years ago by ▴ 370 • written 8.4 years ago by ▴ 10
2
votes
1
reply
2.6k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 8.3 years ago by ▴ 10 • written 9.6 years ago by ▴ 20
2
votes
2
replies
5.2k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 8.5 years ago by ▴ 760 • written 8.5 years ago by ▴ 10
3
votes
8
replies
2.8k
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 8.6 years ago by ★ 6.8k • written 8.6 years ago by • 0
1
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1
reply
1.5k
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 8.7 years ago by 53k • written 8.7 years ago by • 0
5
votes
4
replies
2.1k
views
Contrasts in GOexpress analysis?
gene ontology goexpress
updated 8.8 years ago by ▴ 350 • written 8.8 years ago by ▴ 20
1
vote
2
replies
3.2k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 8.8 years ago by ▴ 760 • written 9.1 years ago by ▴ 10
1
vote
12
replies
4.4k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by ▴ 10
0
votes
3
replies
2.3k
views
piano runGSA with input from DESEQ2
deseq2 gene ontology piano
9.0 years ago simonp.snoeck • 0
1
vote
3
replies
3.0k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 10
1
vote
3
replies
1.4k
views
GoStats ontology count number does not match genes associated with GO term
gostat go terms gene ontology
9.1 years ago adamgetzler • 0
1
vote
2
replies
2.0k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 9.2 years ago by 68k • written 9.2 years ago by • 0
0
votes
3
replies
4.6k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 9.5 years ago by ▴ 350 • written 9.5 years ago by ▴ 130
0
votes
0
replies
1.7k
views
Create list of genes within each GOslim term
gene ontology goslim enrichment analysis gene annotation
9.5 years ago mirko • 0
0
votes
0
replies
1.8k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
9.7 years ago javier.mendoza • 0
57 results • Page 1 of 2
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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