The cancer genome is shaped by various mutational processes over its lifetime, stemming from exogenous and cell-intrinsic DNA damage, and error-prone DNA replication, leaving behind characteristic mutational spectra, termed mutational signatures. This package, sigminer, helps users to extract, analyze and visualize signatures from genome alteration records, thus providing new insight into cancer study.
For pipeline tool, please see its co-evolutionary CLI sigflow.
Copy number signatures:
INDEL (i.e. ID) signatures:
Genome rearrangement signatures:
You can install the stable release of sigminer from CRAN with:
install.packages("BiocManager") BiocManager::install("sigminer", dependencies = TRUE)
You can install the development version of sigminer from Github with:
remotes::install_github("ShixiangWang/sigminer", dependencies = TRUE) # For Chinese users, run remotes::install_git("https://gitee.com/ShixiangWang/sigminer", dependencies = TRUE)
You can also install sigminer from conda
bioconda channel with
# Please note version number of the bioconda release # You can install an individual environment firstly with # conda create -n sigminer # conda activate sigminer conda install -c bioconda -c conda-forge r-sigminer
A complete documentation of sigminer can be read online at
https://shixiangwang.github.io/sigminer-book/. All functions are well
organized and documented at
usage of a specific function
?fun in your R console to see
If you use sigminer in academic field, please cite one of the following papers.
Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 17(5): e1009557. https://doi.org/10.1371/journal.pgen.1009557
Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu, Sigflow: An Automated And Comprehensive Pipeline For Cancer Genome Mutational Signature Analysis, Bioinformatics, btaa895. https://doi.org/10.1093/bioinformatics/btaa895
Please properly cite the following references when you are using any corresponding features. The references are also listed in the function documentation. Very thanks to the works, sigminer cannot be created without the giants.
The software is made available for non commercial research purposes only under the MIT. However, notwithstanding any provision of the MIT License, the software currently may not be used for commercial purposes without explicit written permission after contacting Shixiang Wang email@example.com or Xue-Song Liu firstname.lastname@example.org.
MIT © 2019-Present Shixiang Wang, Xue-Song Liu
MIT © 2018 Anand Mayakonda
Cancer Biology Group @ShanghaiTech
Research group led by Xue-Song Liu in ShanghaiTech University