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```{r setup, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%", warning = FALSE ) ``` # Sigminer: Mutational Signature Analysis and Visualization in R [](https://cran.r-project.org/package=sigminer) [](https://lifecycle.r-lib.org/articles/stages.html) [](https://github.com/ShixiangWang/sigminer/actions) [](https://codecov.io/github/ShixiangWang/sigminer?branch=master) [](https://cran.r-project.org/package=sigminer) [](https://github.com/ShixiangWang/sigminer/issues?q=is%3Aissue+is%3Aclosed) [](https://github.com/ShixiangWang/sigminer) [](https://hits.seeyoufarm.com)  ## Overview 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](https://github.com/ShixiangWang/sigflow). **SBS signatures**: ```{r, fig.width=12, fig.height=5, echo=FALSE, message=FALSE} library(sigminer) load(system.file("extdata", "toy_mutational_signature.RData", package = "sigminer", mustWork = TRUE )) # Show signature profile p1 % as.matrix(), mode = "DBS", style = "cosmic", check_sig_names = F) p3 ``` **INDEL (i.e. ID) signatures**: ```{r fig.width=12, fig.height=5, echo=FALSE} ID = system.file("extdata", "ID_signatures.rds", package = "sigminer", mustWork = TRUE) ID = readRDS(ID) # Show signature profile p4 % as.matrix(), mode = "ID", style = "cosmic", check_sig_names = F) p4 ``` **Genome rearrangement signatures**: ```{r fig.width=10, fig.height=5, echo=FALSE, message=FALSE} p5 . All functions are well organized and documented at . For usage of a specific function `fun`, run `?fun` in your R console to see its documentation. ## Citation 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.*** - ***Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu, Sigflow: An Automated And Comprehensive Pipeline For Cancer Genome Mutational Signature Analysis, Bioinformatics, btaa895***. ------------------------------------------------------------------------ ## Download Stats ```{r, echo=FALSE, warning=FALSE, message=FALSE} library("ggplot2") library("cranlogs") library("dplyr") x ## LICENSE The software is made available for non commercial research purposes only under the [MIT](https://github.com/ShixiangWang/sigminer/blob/master/LICENSE.md). 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 [wangshx\@shanghaitech.edu.cn](mailto:wangshx@shanghaitech.edu.cn) or Xue-Song Liu [liuxs\@shanghaitech.edu.cn](mailto:liuxs@shanghaitech.edu.cn). MIT © 2019-Present Shixiang Wang, Xue-Song Liu MIT © 2018 Anand Mayakonda ------------------------------------------------------------------------ [**Cancer Biology Group**](https://github.com/XSLiuLab) **\@ShanghaiTech** **Research group led by Xue-Song Liu in ShanghaiTech University**