Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) & Alexandrov, Ludmil B., et al. (2020) ). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

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

sigminer is powered by NMF package and maftools package.


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

# Or

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



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).


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


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.


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


sigminer v0.1.11

  • fix #11

sigminer v0.1.10

  • correct year for \doi{10.1038/nature12477}
  • fix #9

sigminer v0.1.9

  • add pheatmap to suggest

sigminer v0.1.8

  • promote get_cnlist function
  • support setting individual component numbers for each feature in get_components function
  • add test_run_components function
  • update author list
  • add package site

sigminer v0.1.7

  • try submitting to CRAN

sigminer v0.1.6

  • update readme & citation & authors
  • export sig_prepare S3 methods
  • promote speed of get_LengthFraction function

sigminer v0.1.5

  • update introduction for package sigminer
  • fix text problem provided by CRAN check team
  • add sig_get_similarity function
  • add toy datasets & update examples
  • fix typo in sig_assign_samples
  • export read_maf
  • update README

sigminer v0.1.4

  • add examples for all exported functions

sigminer v0.1.3

  • add sig_summarize_subtypes function for summarize subtype data
  • add draw_subtypes_comparison function for plotting summarized data from sig_summarize_subtypes function

sigminer v0.1.2

  • add sig_get_correlation function
  • add draw_sig_corrplot function

sigminer v0.1.1

  • add subset.CopyNumber() for subset CopyNumber object
  • add genome_measure slot for CopyNumber object

sigminer v0.1.0

  • Added a NEWS.md file to track changes to the package.
  • Finish basic functions, including
    • read data
    • prepare data
    • estimate signature number
    • extract signatures
    • plot copy number profile
    • plot signature profile
    • plot signature activity
    • ...

Reference manual

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