Genomic Annotation Package?

Hi everyone,

I am new to Julia and BioJulia so this serves as an introduction as well! In my work, I make extensive use of R/Bioconductor and am excited to see the development of BioJulia and am looking to use Julia more in my work.

I was wondering if there exists a functionality provided by a package like ‘biomaRt’ which provides an interface to Ensembl annotation? If not, would there be interest in having such a package? Thanks.


Hello, and welcome!

I’m not familiar with that package in particular and it’s functionality, but you might look at GenomicFeatures.jl.

Well, it sounds like there is interest from at least one person :grinning:. The community here is still small enough that if you desire functionally that doesn’t exist just, you kind of need to build it yourself. This can be both good and bad - you learn a lot from doing this, and the distance between user and developer can me much shorter in Julia than in other languages. If you end up taking this route, definitely don’t hesitate to ask here or on slack if you have questions.

And also, if you want to use Julia, but can’t find a substitute for that package and can’t or don’t want to build it yourself, there’s always RCall.jl, which allows you to run R code directly inside Julia and pass data back and forth.