User: lukeholman

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lukeholman0
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Posts by lukeholman

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Comment: C: How to write a GO Annotation File (GAF) in R
... Well, it's relevant in the sense that there is very likely to be a BioConductor package for making GO slims, and one for saving GO databases in the standard file format, but yeah, close the question if you like. ...
written 10 weeks ago by lukeholman0
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(Closed) How to write a GO Annotation File (GAF) in R
... Hi there, I recently got some help on here downloading an OrgDB using the AnnotationHub package for R. I'd like to transform the GO annotations into a slim version, for example using the command line tool Map2Slim https://github.com/owlcollab/owltools/wiki/Map2Slim. R makes it very easy to download ...
go annotationhub gaf map2slim written 10 weeks ago by lukeholman0
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Comment: C: makeOrgPackageFromNCBI - cannot connect to BioMart
... Great, thanks for the help! I'll have a look into it. Some ideas to improve the help file for makeOrgPackageFromNCBI: - Explain that it is possible to search for available annotation packages using a separate package (AnnotationHub). I thought there were only 20 pre-built packages for the 'classic' ...
written 11 weeks ago by lukeholman0
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makeOrgPackageFromNCBI - cannot connect to BioMart
... Hey there, I'm having some trouble getting makeOrgPackageFromNCBI() to work. As you can see from the output below, it downloads the data from NCBI just fine, then fails when trying to access BioMart. When I click that BioMart link in the error message, there is just a blank webpage with the text 0. ...
annotationforge written 12 weeks ago by lukeholman0 • updated 12 weeks ago by James W. MacDonald48k

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