GenomicFeatures
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Bioconductor
Conveniently import and query gene models
Thank you for developing such a powerful package for working with genomes in R. My questions is how do I import pseudogenes, e.g. MTCO2P2, from a NCBI RefSeq human assembly...
Added weights to coverage by transcript, I have not made this work for GAlignmentList, only GAlignment and GAlignmentPairs. So maybe we discuss what to do with that one ?
I experienced an error similar to one reported on the [support site](https://support.bioconductor.org/p/9141351/). Incorrect annotations are returned when calling a VariantAnnotation function (`locateVariants()` with `region = IntronVariants()` ) that internally uses...
For human data, using human NGS reads (1.4GB) as GRanges: ``` # Using reduced data that has a score column for duplicated reads, # every unique read is only once....
There is some strange behavour on how it handles names in the transcripts: Sorry for bad test data, made this quickly: tx is a GRangesList of 100.000 transcripts: ranges is...
See https://support.bioconductor.org/p/101245/
Relatively recently, `GenomicFeatures::makeTxDbFromEnsembl` stopped working for Human. I'm using 1.54.1, but the relevant code hasn't haven in 1.56 or in txdbmaker ``` txdb
