5 votes
Accepted

Is there a JSON-based genomic feature format?

JVCF is a JSON schema for describing genetic variants. BioJSON is a JSON schema for multiple sequence alignments. The output of mygene.info's gene annotation web service is JSON-formatted. You might ...
user avatar
1 vote
Accepted

GenomicRanges: get nearest neighbor distances for random genes using a for loop

Is it because rand.gr has not been initialised, so when you ask to set rand.gr[i] it can't because there isn't one yet? If you set i to a value (e.g. 1), and run the lines inside your loop, which of ...
user avatar
1 vote

Is there a JSON-based genomic feature format?

I've written a Python library called PyReference which converts a GTF / GFF (RefSeq and Ensembl) into a gzipped JSON file. You can just use this if you like but there's also a Python wrapper around ...
user avatar
1 vote

Is there a JSON-based genomic feature format?

BioJS has capacity to read and write GFF as streams, it might have something of interest such as this: https://github.com/biojs-io/biojs-io-gff
user avatar

Only top scored, non community-wiki answers of a minimum length are eligible