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Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. To evaluate the mutational signatures operative in a cancer genome, one first needs to quantify …

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, …

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using …

A neural network for determination of latent dimensionality in non-negative matrix factorization

Classical density functional analysis of the ionic size effects on the properties of charge regulating electric double layers

Finding the number of latent topics with semantic non-negative matrix factorization

Improved protein decoy selection via non-negative matrix factorization

Distributed non-negative matrix factorization with determination of the number of latent features

Identification of anomalous diffusion sources by unsupervised learning

Solvophilic and solvophobic surfaces and non-Coulombic surface interactions in charge regulating electric double layers