License and citation

License

SigMA2 is distributed under Harvard's Academic and Non-Commercial Research Use license. In short: use it for academic and non-commercial research; do not redistribute it; do not use it commercially without a license from Harvard's Office of Technology Development (otd@harvard.edu); and attribute it as the license's §7 asks. The license text ships with the package.

Citation

The SigMA2 manuscript is in preparation; a citation will be given here when it is out. Until then, cite the method it builds on:

Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJ. Detecting the mutational signature of homologous recombination deficiency in clinical samples. Nature Genetics 51, 912–919 (2019). doi:10.1038/s41588-019-0390-2

and name the SigMA2 release you ran (sigma2 info prints it; out.df runs record it in their log lines as v0.0.16-alpha.20).

Third-party data behind the models

The msk HRD and MMRD/POLE models were trained on MSK-IMPACT data released under CC BY-NC-ND; derived material inherits that license.
The example files used in these pages (fifty MSK-IMPACT breast panels, a TCGA breast MAF) are SigMA (R)'s example data, under SigMA's license, from the SigMA repository.
The GEL (Genomics England) genomes the breast, lung, colorectal, prostate and skin classifiers were trained on are not redistributed in any form; the classifiers are models, not data.

Status of the repository

The SigMA2 source repository is private while the manuscript is in preparation, so the Repository link in the package metadata returns 404 to outsiders and sigma2 data fetch works only for a GitHub account the maintainers have given access; the repeat-locus files it fetches are also in the public SigMA (R) repository. The package itself installs from PyPI without credentials.

License and citation

License

Citation

The SigMA2 manuscript is in preparation; a citation will be given here when it is out. Until then, cite the method it builds on:

Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJ. Detecting the mutational signature of homologous recombination deficiency in clinical samples. Nature Genetics 51, 912–919 (2019). doi:10.1038/s41588-019-0390-2

and name the SigMA2 release you ran (sigma2 info prints it; out.df runs record it in their log lines as v0.0.16-alpha.20).

Third-party data behind the models

The msk HRD and MMRD/POLE models were trained on MSK-IMPACT data released under CC BY-NC-ND; derived material inherits that license.
The example files used in these pages (fifty MSK-IMPACT breast panels, a TCGA breast MAF) are SigMA (R)'s example data, under SigMA's license, from the SigMA repository.
The GEL (Genomics England) genomes the breast, lung, colorectal, prostate and skin classifiers were trained on are not redistributed in any form; the classifiers are models, not data.