Questions tagged [genomefeatures]

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Is there a JSON-based genomic feature format?

There's a variety of formats for storing genomic features (e.g. Genbank, GFF, GTF, Bedfile) but all of the ones that I'm familiar with use either a custom format (Genbank) or a CSV with defined column ...
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2x2 contingency for genomic feature enrichment

I have an enhancer list and I would like to see how it overlaps with histone lists from different cell types (different sizes) significantly. I would like to use a contingency table for testing but ...
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2 answers

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

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
2 votes
0 answers

How to create custom txDb using GenomeFeatures?

I have orf virus sequence in GFF3 format. I am trying to create a txDb using GenomicFeatures::makeTxDbFromGFF() function. But, it is not able to capture any CDS: <...