SigProfilerExtractor

SigProfilerExtractor is a python framework that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting, seamlessly integrating with other SigProfiler tools.

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Citation

S.M.A. Islam, Y. Wu, M. Díaz-Gay, E.N. Bergstrom, Y. He, M. Barnes, M. Vella, J. Wang, J.W. Teague, P. Clapham, S. Moody, S. Senkin, Y.R. Li, L. Riva, T. Zhang, A.J. Gruber, R. Vangara, C.D. Steele, B. Otlu, A. Khandekar, A. Abbasi, L. Humphreys, N. Syulyukina, S.W. Brady, B.S. Alexandrov, N. Pillay, J. Zhang, D. J. Adams, I. Marticorena, D.C. Wedge, M.T. Landi, P. Brennan, M.R. Stratton, S. G. Rozen, L.B. Alexandrov, Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor, BioRxiv (2020) 1–47, https://doi.org/10.1101/2020.12.13.422570.

License

This software and its documentation are copyright 2018 as a part of the SigProfiler project. The SigProfilerExtractor 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

All SigProfilerGenerator related queries or bug reports should be directed to S M Ashiqul Islam (Mishu) at sislam6@albany.edu.