Finding genome wide annotation R package

Question

[Za]

Hi,

I need something like GO.db, org.Mm.xx and org.Hs.xx for my organism as exist for muse and human in https://bioconductor.org/packages/release/BiocViews.html#___AnnotationData but for my organism I only can find MeSH.Ddi.AX4.eg.db

My organism is Dictyostelium discoideum, do you know how I can find and install genome wide annotation for this organism?

[Ram]

Is the dictybase biomart useful at all?

[Za]

Thank you, actually for package CellRouter I need these annotation as igraph package uses that for GRN construction while I don't know how to use gff3 or another zip files for annotation. CellRouter itself uses org.Hs.eg.db or org.Mm.eg.db internally for human and mouse. I don't know how to compensate for my organism in lack of such a package

[mmfansler]

The service on dictybase.org looks broken to me, and connecting via biomaRt package doesn't seem to work either.

[Za]

Excuse me, if there is a list of transcription factors in this organism that will compensate for genome wide annotation for CellRouter software. In in this address likely there are transcript factors http://www.transcriptionfactor.org/index.cgi?Download but I am not sure how I obtain them or you know how to provide a list of transcription factors in this organism?

[mmfansler]

I've never used CellRouter, but their examples show method signatures requiring Bioconductor Organism Packages, so: No, I don't think you can simply substitute a list of TFs.

Have you had a look at the vignette I referenced in my answer? Using the NCBI route, all it requires is the Taxonomy ID, Genus, and Species. For the more manual method, the dictybase.org Downloads section looks like it has everything you need: Gene IDs, Symbols, Genomic Coordinates (GFF/GTF), and GO annotations.

Answer 1

[mmfansler]

If you can't find an existing package/service, you can generate annotation database objects using the AnnotationForge package. There is a vignette specifically on constructing org.xx.eg.db packages.