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    <section class="page-title"><div class="section"><span class="eyebrow">Tools</span><h1>SigProfilerSuite tools</h1><p>The suite covers the main steps of mutational signature analysis, from mutation categorization and visualization to <em>de novo</em> extraction, decomposition, assignment, simulation, clustered mutation detection, and genomic topography.</p></div></section>
    <section class="section"><div class="grid grid-2"><article class="card tool-card lab-ualbany">
          <span class="tag">Matrix generation</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerMatrixGenerator.png" alt="SigProfilerMatrixGenerator logo">
          <h3>SigProfilerMatrixGenerator</h3>
          <p>Generates mutational matrices from somatic mutation data across supported mutation classes and mutational contexts.</p>
          <p><span class="kbd">pip install SigProfilerMatrixGenerator</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerMatrixGenerator/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerMatrixGenerator/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator/issues">Issues</a></div>
        </article><article class="card tool-card lab-ualbany">
          <span class="tag">Visualization</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerPlotting.png" alt="SigProfilerPlotting logo">
          <h3>SigProfilerPlotting</h3>
          <p>Creates standardized visualizations of mutational catalogues, signatures, decompositions, and sample-level contributions.</p>
          <p><span class="kbd">pip install sigProfilerPlotting</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerPlotting">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerPlotting/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerPlotting/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerPlotting/issues">Issues</a></div>
        </article><article class="card tool-card lab-ualbany">
          <span class="tag"><em>De novo</em> signature extraction</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerExtractor.png" alt="SigProfilerExtractor logo">
          <h3>SigProfilerExtractor</h3>
          <p>Extracts <em>de novo</em> mutational signatures from mutational matrices and estimates their activities in individual samples.</p>
          <p><span class="kbd">pip install SigProfilerExtractor</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerExtractor">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerExtractor/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerExtractor/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerExtractor/issues">Issues</a></div>
        </article><article class="card tool-card lab-cnio">
          <span class="tag">Signature decomposition and assignment</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerAssignment.png" alt="SigProfilerAssignment logo">
          <h3>SigProfilerAssignment</h3>
          <p>Decomposes <em>de novo</em> signatures into reference signatures and assigns known or custom signatures to samples and individual mutations.</p>
          <p><span class="kbd">pip install SigProfilerAssignment</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerAssignment">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerAssignment/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerAssignment/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerAssignment/issues">Issues</a></div>
        </article><article class="card tool-card lab-cnio">
          <span class="tag">Simulation and null models</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerSimulator.png" alt="SigProfilerSimulator logo">
          <h3>SigProfilerSimulator</h3>
          <p>Generates realistic simulated mutational landscapes for benchmarking, clustered-mutation analysis, and topography-related null models.</p>
          <p><span class="kbd">pip install SigProfilerSimulator</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerSimulator">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerSimulator/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerSimulator/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerSimulator/issues">Issues</a></div>
        </article><article class="card tool-card lab-cnio">
          <span class="tag">Clustered mutations</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerClusters.png" alt="SigProfilerClusters logo">
          <h3>SigProfilerClusters</h3>
          <p>Detects clustered and non-clustered mutations and classifies clustered events such as DBS, MBS, omikli, and kataegis.</p>
          <p><span class="kbd">pip install SigProfilerClusters</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerClusters">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerClusters/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerClusters/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerClusters/issues">Issues</a></div>
        </article><article class="card tool-card lab-metu">
          <span class="tag">Genomic topography</span>
          <img class="tool-logo" src="assets/img/logos/SigProfilerTopography.png" alt="SigProfilerTopography logo">
          <h3>SigProfilerTopography</h3>
          <p>Evaluates the spatial distribution of mutational processes relative to chromatin, replication, transcription, and strand-associated genomic features.</p>
          <p><span class="kbd">pip install SigProfilerTopography</span></p>
          <div class="card-actions"><a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerTopography">GitHub</a> <a class="button-secondary" href="https://pypi.org/project/SigProfilerTopography/">PyPI</a> <a class="button-secondary" href="https://sigprofilersuite.github.io/SigProfilerTopography/">Documentation</a> <a class="button-secondary" href="https://github.com/SigProfilerSuite/SigProfilerTopography/issues">Issues</a></div>
        </article></div></section>
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