umccr / RNAsum

Pipeline for generating RNAseq-based cancer patient reports
https://umccr.github.io/RNAsum/
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Use AnnotationHub to access ensembldb #102

Closed skanwal closed 9 months ago

skanwal commented 1 year ago

Draft PR:

To discuss

skanwal commented 1 year ago

@pdiakumis - as discussed in our 1-1 last week, moved database logic to R script and updated rmd as well.

skanwal commented 1 year ago

Tested locally on my machine and the code works with the rds file under inst/extdata/tx_gene_id_105.rds.

Comparing reports between rnasum-rpackage and update/ensembldb branches next.