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[DEPRECIATED/OUTDATED] CopyKit Paper (BioRxiv Version)

This repository contains the step-by-step RMarkdown tutorials and scripts corresponding to the BioRxiv preprint version of the manuscript: "Resolving clonal substructure from single cell genomic data using CopyKit".

Resolving clonal substructure from single cell genomic data using CopyKit > Darlan Conterno Minussi, et al.
bioRxiv (2022).
DOI: 10.1101/2022.03.09.483497

⚠️ Note on Manuscript Versions:

  • For the Published Manuscript: The code, benchmarking, and processing scripts for the final peer-reviewed publication are located in our new repository:
    👉 navinlabcode/Copykit_manuscript_code
  • For Tutorials: We maintain this repository because it provides a comprehensive, step-by-step RMarkdown workflow that serves as an excellent educational resource for learning how to use CopyKit.

RMarkdown Tutorial (BioRxiv)

You can view the rendered step-by-step tutorial for the BioRxiv manuscript here:
https://navinlabcode.github.io/CopyKit_paper/

CopyKit installation

You can install the development version of CopyKit from github with:

devtools::install_github("navinlabcode/copykit")

Please check CopyKit package GitHub repository as well: https://github.com/navinlabcode/copykit

Documentation

CopyKit complete documentation can be found here: https://navinlabcode.github.io/CopyKit-UserGuide/

Datasets

Files used for this project are deposited to the sequence read archive (SRA) under BioProject PRJNA785341.