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ampliconarchitect

Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.

cnvmatrixgenerator

Mutational Signatures for copy number alterations

epigenomics_cwl

hrd-signatures

Detecting Homologous Recombination Deficiency with mutational signatures

methylation-project

predicting-epl-standings

sigprofilerassignment

Assignment of known mutational signatures to individual samples and individual somatic mutations

sigprofilerextractor

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 SigProfilerMatrixGenerator and SigProfilerPlotting.

sigprofilermatrixgenerator

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.

sigprofilermatrixgeneratorr

R wrapper for utilizing the SigProfilerMatrixGenerator framework

sigprofilerplotting

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.

sigprofilersensitivity

Tool to simulate mutational signature injection into samples to assess sensitivity of detection

svmatrixgenerator

tomotopy

Python package of Tomoto, the Topic Modeling Tool