Showing : go • reset
0
votes
1
reply
221
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 6 weeks ago by ▴ 40 • written 6 weeks ago by • 0
1
vote
3
replies
325
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 10
0
votes
2
replies
346
views
GO enrichment analysis does not show any pathways in my case
GO EnrichmentBrowser
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
4
replies
524
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago • updated 5 months ago Rockbar • 0
1
vote
1
reply
402
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 6 months ago by 65k • written 7 months ago by • 0
0
votes
1
reply
598
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
0
replies
444
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
12 months ago Priya • 0
0
votes
2
replies
712
views
GO analysis in R vs website
GO RNASeq
13 months ago Nitro • 0
1
vote
4
replies
1.2k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
13 months ago S ▴ 10
1
vote
1
reply
1.0k
views
topGo error loading data
topGO GO
16 months ago peter • 0
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 16 months ago by • 0
0
votes
1
reply
581
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 17 months ago by ▴ 10 • written 17 months ago by • 0
0
votes
1
reply
664
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db GOfuncR GO GOSim goProfiles
updated 18 months ago by ▴ 760 • written 18 months ago by • 0
0
votes
0
replies
511
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
18 months ago BioinFo.X • 0
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
18 months ago dario.beraldi • 0
2
votes
3
replies
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 18 months ago by ▴ 120 • written 19 months ago by ▴ 10
1
vote
3
replies
1.6k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 22 months ago by 65k • written 22 months ago by ▴ 60
0
votes
13
replies
2.8k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 23 months ago by ★ 3.9k • written 23 months ago by ▴ 10
0
votes
0
replies
572
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
2.0 years ago theophile • 0
0
votes
0
replies
2.9k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
2.1 years ago Raito92 ▴ 60
15
votes
18
replies
3.3k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 60
1
vote
2
replies
1.2k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
2.1 years ago Adelyn ▴ 10
0
votes
1
reply
1.2k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.2 years ago by ★ 3.9k • written 2.2 years ago by • 0
0
votes
3
replies
1.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 90
2
votes
3
replies
1.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 2.4 years ago by 65k • written 2.4 years ago by ▴ 20
2
votes
6
replies
1.4k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 2.7 years ago by ★ 6.5k • written 2.7 years ago by • 0
0
votes
1
reply
733
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
2
votes
2
replies
981
views
retrieve gene IDs from GO.db GO
GO GO.db
3.0 years ago • updated 2.9 years ago decppced • 0
0
votes
9
replies
1.7k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 2.9 years ago by 65k • written 3.0 years ago by • 0
2
votes
2
replies
2.6k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
3.1 years ago Wuschel ▴ 10
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
2
votes
0
replies
916
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error topGO go
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
4
votes
1
reply
5.9k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 30
0
votes
0
replies
604
views
ViseaGO merge_enrich_terms ERROR
go
3.8 years ago zaza.inline • 0
0
votes
9
replies
1.5k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.8 years ago camillab. ▴ 10
2
votes
2
replies
857
views
biomart webservice error when using data from Phytozome
software error go
3.8 years ago e.lopez-cortegano • 0
0
votes
1
reply
788
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 10
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
3.9 years ago Ruixuan ▴ 10
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 14 months ago by 65k • written 3.9 years ago by ▴ 30
0
votes
5
replies
1.2k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
3.9 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
892
views
About topGO error
go
updated 4.0 years ago by ▴ 30 • written 4.0 years ago by • 0
2
votes
4
replies
1.4k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
4.0 years ago liz.marjory • 0
0
votes
2
replies
680
views
GO analysis without gene IDs?
deseq2 annotation go
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 60
0
votes
0
replies
588
views
enrichplot pakage no output plot
go
4.0 years ago Hamidreza Hashemi ▴ 20
2
votes
1
reply
5.1k
views
GO of clusterprofiler
go
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO GO
4.0 years ago Al-a ▴ 10
5
votes
7
replies
2.1k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
6
votes
6
replies
2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Votes
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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