Published November 27, 2025
| Version 1.0
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Skrupskelyte etal SI code: Publication supporting code and notebooks
Authors/Creators
-
1.
Wellcome Sanger Institute
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2.
University of Cambridge
Description
This repository contains R code used to produce copynumber analyses and figures for the supplementary information accompanying Skrupskelyte et al.
Files
qdnaseq_call_offtarget_read_cn.R - Main R script to call copynumber.
Detailed run instructions and dependencies can be found at: https://github.com/PHJonesGroup/Skrupskelyte_etal_SI_code and also in the Readme file here
README.md - Run and installation instructions for copy number calling script
Copynumber_parameter_sweep.ipynb & Copynumber_parameter_sweep.html - Validations of the settings used to call copy number in the above main Rscript
/References - Contains the Co-ordinate BED file used for calling and sequencing in this publication
/Figures - PDF of the read counts across chromosomes from the parameter sweeps
Files
PHJonesGroup/Skrupskelyte_etal_SI_code-1.0.zip
Files
(3.2 MB)
| Name | Size | Download all |
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md5:010106c36c527242aaf4577e4359afc1
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3.2 MB | Preview Download |
Additional details
Related works
- Is supplement to
- Software: https://github.com/PHJonesGroup/Skrupskelyte_etal_SI_code/tree/1.0 (URL)
Software
- Repository URL
- https://github.com/PHJonesGroup/Skrupskelyte_etal_SI_code
- Programming language
- R , Jupyter Notebook