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SigProfilerAssignment

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SigProfilerAssignment is a Python framework that assigns and decomposes mutational signatures in individual samples and individual somatic mutations.

Refitting of mutational signatures is a numerical optimization approach that not only identifies the set of operative mutational signatures in a particular sample, but also quantifies the number of mutations attributed to each signature detected in that sample. In addition to refitting reference signatures, the tool have an advanced mode that can assign de novo extracted signatures and decompose them into reference signatures, facilitating biological interpretation and comparison with established catalogs.

It supports multiple mutation contexts and genome builds, provides confidence estimation and signature activity thresholds, and generates detailed visual and tabular outputs to aid downstream analyses. The tool refits different types of known reference mutational signatures, including COSMIC SBS, DBS, ID, and CN signatures, as well as custom signature databases.

SigProfilerAssignment makes use of SigProfilerMatrixGenerator and SigProfilerPlotting, enabling seamless integration with other tools in the SigProfiler suite.

The SigProfilerAssignment library is available on GitHub and PyPI

Citation

Díaz-Gay M, Vangara R, Barnes M, Wang X, Islam SMA, Vermes I, Duke S, Narasimman NB, Yang T, Jiang Z, Moody S, Senkin S, Brennan P, Stratton MR, Alexandrov LB. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. Bioinformatics. 2023;39(12):btad756. https://doi.org/10.1093/bioinformatics/btad756

License

This software and its documentation are part of the SigProfiler project and are copyrighted © 2022. The SigProfilerAssignment framework is free software and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Contact

For questions, support requests, or bug reports, please contact the SigProfilerSuite team via GitHub issues or by email at contact@sigprofilersuite.org.