Bioconductor Biomart

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clusterProfiler OrgDb biomaRt Zea_mays

updated 5 days ago by James W. MacDonald 65k • written 5 days ago by sansan • 0

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biomart rnaseq

written 5.2 years ago by jarod_v6@libero.it ▴ 40

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biomaRt

updated 5 days ago by James W. MacDonald 65k • written 5 days ago by bas_work ▴ 30

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biomaRt

updated 22 days ago by James W. MacDonald 65k • written 22 days ago by Reeya • 0

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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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