scarHRD what to do without sequenza

Hi, I'm trying to install scarHRD but since there is not sequenza package available nowadays, I got installing scarHRD the error: ERROR: dependency ‘sequenza’ is not available for package ‘scarHRD’ ─ removing ‘/tmp/RtmpeWcghn/Rinst284cb4536be01/scarHRD’ ----------------------------------- ERROR: package installation failed Error: Failed to install 'scarHRD' from GitHub: ! System command 'R' failed What can I do? Moreover, I want to run scarHRD by using ASCAT output, not sequenza... Thanks!

Sep 29 '23 15:09 ldelgado-serrano

Bump - (checking if tool is maintained)

Oct 26 '23 16:10 DolapoA

sequenza may have moved to another website, and you can get it from conda too

Oct 27 '23 19:10 jwuatx

The underlying issue is the package copynumber which got deprecated on Bioconductor as the vignette didn't compile anymore and the maintainer did not respond.

However, you can install copynumer and sequenza using these two commands (also works on R 4.3):"

devtools::install_github("buschlab/copynumber", build_vignettes = FALSE)
devtools::install_version("sequenza", version = "3.0.0", repos = "http://cran.us.r-project.org")

Nov 13 '23 20:11 nr23730