wuyangff95 / synsigeval

SynSigEval

Assess the performance of mutational-signature analysis programs using catalogs of synthetic mutational spectra created by package SynSigGen.

This version (0.4.0) and previous version (0.3.1) are suitable for assessing the extraction accuracy in paper mSigHdp: hierarchical Dirichlet processes for mutational signature discovery - Liu et al. (2022).

For assessing extraction accuracy on data sets presented by paper Accuracy of Mutational Signature Software on Correlated Signatures - Wu et al. (2022), please proceed to version 0.2.2.

Check NEWS.md for differences between version 0.4.0 and previous versions.

Installation

Before installation, prerequisites in Bioconductor needs to be installed:

install.packages("BiocManager")
BiocManager::install(
  c("Biostrings", "BSgenome", "GenomeInfoDb", "GenomicRanges")
)

Install the development version of SynSigEval from GitHub with the R command line:

install.packages("remotes")
# Stable version
remotes::install_github("WuyangFF95/SynSigEval", ref = "v0.4.0-branch")
# Develop version
remotes::install_github("WuyangFF95/SynSigEval", ref = "main")

Reference manual

https://github.com/WuyangFF95/SynSigEval/blob/main/data-raw/SynSigEval_0.4.0.pdf