copynumber with hg38/mm10/mm39

This is an updated version of the copynumber R package. It has been modified to support the human hg38 and mouse mm10 and mm39 genome builds.

Installation

You can install the package from R-universe (pre-compiled binary):

BiocManager::install("copynumber", site_repository = "https://igordot.r-universe.dev")

Alternatively, you can install from source (slower):

BiocManager::install("igordot/copynumber")

About

This fork of copynumber adds the following improvements to the original Bioconductor package:

• Support for more recent genome builds, used by the assembly parameter in aspcf(), multipcf(), pcf(), and winsorize()
• A documentation website (via roxygen2 and pkgdown)
• A clean, browsable HTML vignette (via knitr and R Markdown)
• Automated tests to help ensure that the package continues to function

This modification builds upon the previous work of aroneklund and ShixiangWang. There is an additional fork by Irrationone that provides a species-agnostic approach, but the enhanced functionality adds a new parameter that makes it not backward compatible. Any packages that depend on copynumber (such as sequenza, PureCN, or scarHRD) would need to be modified as well to take advantage of the new feature.

This fork is based on copynumber 1.29.0. The package was removed in Bioconductor 3.18 (released October 2023). There have been no changes to the code besides Bioconductor-mandated version bumps since 2013.

Please use GitHub issues to report any problems or request new features.