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Bioconductor / AnnotationForge

Tools for building SQLite-based annotation data packages
https://bioconductor.org/packages/AnnotationForge
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Forge OrgDb package #16

Closed imalsoft9 closed 3 years ago

imalsoft9 commented 3 years ago

I need to create annotation package like (org.Hs.eg.db) for two organisms: 1-Galleria mellonella ASM364042v2 2-Madurella mycetomatis ASM127576v2\ Both genomes are assembled in scaffolds level For the Galleria Mellonella there is org.Galleria_mellonella.eg.sqlite in AnnotationHub library but not for the Madurella Mycetomatis. I appreciate if you give guidelines or point to resource that I can follow to create OrgDb for the two genomes. the purpose was to use the OrgDb for gene set enrichment analysis.

lshep commented 3 years ago

There are two AnnotationForge functions for creating your own OrgDb. Please check out AnnotationForge::makeOrgPackage and/or AnnotationForge::makeOrgPackageFromNCBI. If you run into additional issues I highly suggest posting to the bioconductor support site instead of github issues. The support site reaches the larger community base that might have additional solutions and faster attention. Github issues more for reporting coding errors/bugs that need correcting. support.bioconductor.org Cheers!