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Showing :
orgdb
•
reset
2
votes
4
replies
514
views
Need help generating BSgenome and orgdb
OrgDb
BSgenome
6 months ago • updated 11 weeks ago
mat149
▴ 70
1
vote
3
replies
446
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
j_denton
• 0
0
votes
5
replies
188
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 2 hours ago by
James W. MacDonald
65k • written 2 days ago by
Gayatri
• 0
2
votes
1
reply
186
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 4 weeks ago by
enee
▴ 10
2
votes
2
replies
136
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
sansan
• 0
5 results • Page
1 of 1
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Replies
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error
by
James W. MacDonald
65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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