/Clonalscope

Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalscope is able to detect subclones, label malignant cells, and trace subclones for both scRNA-seq and ST data.

Primary LanguageR

Clonalscope

Chi-Yun Wu, Jiazhen Rong, Zhang Lab, University of Pennsylvania

Description

Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalscope leverages prior information from matched bulk DNA-seq data, and implements a nested Chinese Restaurant Process to model the evolutionary process in tumors. Clonalscope is able to detect subclones, label malignant cells (with the help of matched WGS/WES data), and trace subclones for both scRNA-seq and ST data.

For more information about the method, please check out the manuscript.

Overview of Clonalscope

Install

  • You can install Clonalscope with the code below:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
install.packages("devtools")
options(timeout=9999999)
devtools::install_github("seasoncloud/Clonalscope") # install
library(Clonalscope) # load

# It takes <5 mins for the installation.

  • You can download example datasets for Clonalscope with the following command:

    Using terminal, download the repository.

    git clone https://github.com/seasoncloud/Clonalscope.git

  • We have included example data in the folder data-raw/.

Detailed tutorials with example datasets

  • Click the links below to read detailed tutorials for different data types.
  1. scRNA-seq subclone detection and malignant cell labeling
  2. Spatial Transcriptomic subclone detection
  3. Spatial Transcriptomic subclone tracing
  4. scRNA-seq subclone detection and malignant cell labeling without paired WGS/WES

Citation

Wu, C.-Y. et al. Cancer subclone detection based on DNA copy number in single cell and spatial omic sequencing data. bioRxiv (2022): https://doi.org/10.1101/2022.07.05.498882