Retrotransposed Transcripts and Mitochondrial Fusions Functions Missing from Bioconductor Download

PapenfussLab / StructuralVariantAnnotation

R package designed to simplify structural variant analysis

GNU General Public License v3.0

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Retrotransposed Transcripts and Mitochondrial Fusions Functions Missing from Bioconductor Download #32

Closed DarioS closed 3 years ago

DarioS commented 3 years ago

I installed using install("StructuralVariantAnnotation") and installed version 1.6.0. But, it's missing rtDetect and numtDetect. NEWS file contains only:

Changes in version 0.99.0 (2019-04-05)
+ Submitted to BioConductor

so it's unclear to the end-user why this functionality was recently removed from the package. Does LINX supersede it?

d-cameron commented 3 years ago

They got pulled out into their own package.

@jackieduckie: what's the status on the refactoring. Are they in BioConductor yet?

jackieduckie commented 3 years ago

They are under revision and will be made publicly available soon.

DarioS commented 3 years ago

Any plans for retrotransposon annotation, such as T.S.D. or source and destination coordinates based on transduction sequences?

jackieduckie commented 3 years ago

@DarioS RTDetect should be submitted to BioConductor as a seperate package within a few weeks time. Hope that helps.