SigProfilerExtractor 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 SigProfilerMatrixGen…

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

Sigflow: Streamline Analysis Workflows for Mutational Signatures, https://github.com/ShixiangWang/sigflow/pkgs/container/sigflow

SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.

R wrapper for utilizing the SigProfilerMatrixGenerator framework

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

highly-efficient & lightweight mutation signature matrix aggregation

SigMa is a probabilistic model for the sequential dependencies of mutation signatures

An R wrapper for SigProfilerExtractor 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 o…

Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.

Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/

An R wrapper for running the SigProfilerPlotting framework

R package for bayesNMf, a computationally efficient Gibbs sampler for Bayesian Poisson NMF which automatically determines the number of latent factors while quantifying uncertainties of the learned matrices.

Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures

Comprehensive cancer signatures with reusable modules written in python, integrating SNV, SV and MSI profiles in signatures decomposed using non-negative matrix factorisation, and produce production ready pdf reports.

Some workflows I wrote for my phd projects