How to extract all annotations in a genomic range from NCBI using R?
Entering edit mode
3.3 years ago
Solowars ▴ 70

Hello all,

I want to study the genes in the neighbourhood of a number of genes of interest across multiple species. For several reasons, I chose to use NCBI annotations for this task, and I'm playing around with R and dedicated packages, such as rentrez, which can achieve many cool things.

However, I couldn't find a way to, for example, specify assembly, species, chromosome and search coordinates and get back a file (or a list for that matter) containing the corresponding gene annotations of all genes annotated in the specific region.

I wanted to know, in case somebody with more NCBI experience than me reads this, if this task is achievable using R tools or not (so I can invest my time searching for another way to do it).

NB.: I know that doing this should be relatively trivial using Ensembl and biomaRt, but I'd rather do it using NCBI, if possible.

Thank you so much for your thoughts and consideration.


R rentrez NCBI Synteny comparative genomics • 696 views

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