Skip to content
🌲 A uniform interface for genomic variation signature analysis and visualization in R
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
data
docs
inst
man
tests
vignettes
.Rbuildignore
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
README.Rmd
README.md
appveyor.yml
codecov.yml
sigminer.Rproj

README.md

sigminer logo

CRAN status lifecycle AppVeyor build status Travis build status Coverage status emoji-log

Overview

The goal of sigminer is to provide a uniform interface for genomic variation signature analysis and visualization.

sigminer is powered by NMF package and maftools package.

Installation

You can install the stable release of sigminer from CRAN with:

install.packages("sigminer")
# Or
BiocManager::install("sigminer")

You can install the development version of sigminer from Github with:

remotes::install_github("ShixiangWang/sigminer")

Citation

If you use sigminer in academic field, please cite:

Wang, Shixiang, et al. "The predictive power of tumor mutational burden 
    in lung cancer immunotherapy response is influenced by patients' sex."
    International journal of cancer (2019).

and

Gaujoux, Renaud, and Cathal Seoighe. "A Flexible R Package for 
    Nonnegative Matrix Factorization."" BMC Bioinformatics 11, no. 1 (December 2010).

Acknowledgments

The code for extracting copy number signatures was based in part on the source code from paper Copy number signatures and mutational processes in ovarian carcinoma, if you use this feature, please also cite:

Macintyre, Geoff, et al. "Copy number signatures and mutational
    processes in ovarian carcinoma." Nature genetics 50.9 (2018): 1262.

The code for extracting mutational signatures was based in part on the source code of the maftools package, if you use this feature, please also cite:

Mayakonda, Anand, et al. "Maftools: efficient and comprehensive analysis
    of somatic variants in cancer." Genome research 28.11 (2018): 1747-1756.

LICENSE

MIT © 2019 Shixiang Wang, Geoffrey Macintyre, Xue-Song Liu

You can’t perform that action at this time.