SigProfilerAssignment 1.1.4

Mutational signatures attribution and decomposition tool

SigProfilerAssignment

SigProfilerAssignment enables assignment of previously known mutational signatures to individual samples and individual somatic mutations. The tool refits different types of reference mutational signatures, including COSMIC signatures, as well as custom signature databases. SigProfilerAssignment makes use of SigProfilerMatrixGenerator and SigProfilerPlotting, seamlessly integrating with other in SigProfilerSuite.

Documentation

Detailed documentation can be found at https://sigprofilersuite.github.io/SigProfilerAssignment.

Quick Start Guide

Installation

Install the current stable PyPi version of SigProfilerAssignment:

$ pip install SigProfilerAssignment

If mutation calling files (MAF, VCF, or simple text files) are used as input, please install your desired reference genome as follows (available reference genomes are: GRCh37, GRCh38, mm9, mm10, rn6, and rn7):

$ python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37')

Running

Assignment of known mutational signatures to individual samples is performed using the cosmic_fit function. Input samples are provided using the samples parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files, or mutational matrices. COSMIC mutational signatures v3.5 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the cosmic_version and signature_database parameters. Results will be found in the folder specified in the output parameter.

from SigProfilerAssignment import Analyzer as Analyze
Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96")

You can also run SigProfilerAssignment cosmic_fit function from command line:

$ SigProfilerAssignment cosmic_fit samples output --input_type "matrix" --context_type "96"

Reference

Díaz-Gay M, Vangara R, Barnes M, et al., 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

Contact

For questions, support requests, or bug reports, please contact the SigProfilerSuite team via GitHub issues or by email at [e-mail].