.gitignore
CHANGELOG.md
Dockerfile
LICENSE.txt
MANIFEST.in
README.md
install_genome.py
mkdocs.yml
mkdocs_hooks.py
pyproject.toml
setup.py
test.py
.github/workflows/ci.yml
.github/workflows/create-version-tag.yml
.github/workflows/docs.yml
.github/workflows/release.yml
.github/workflows/static.yml
SigProfilerExtractor/__init__.py
SigProfilerExtractor/_version.py
SigProfilerExtractor/estimate_best_solution.py
SigProfilerExtractor/nmf_cpu.py
SigProfilerExtractor/nmf_gpu.py
SigProfilerExtractor/nndsvd.py
SigProfilerExtractor/sigpro.py
SigProfilerExtractor/sigprofilerextractor_cli.py
SigProfilerExtractor/subroutines.py
SigProfilerExtractor/version.py
SigProfilerExtractor.egg-info/PKG-INFO
SigProfilerExtractor.egg-info/SOURCES.txt
SigProfilerExtractor.egg-info/dependency_links.txt
SigProfilerExtractor.egg-info/entry_points.txt
SigProfilerExtractor.egg-info/not-zip-safe
SigProfilerExtractor.egg-info/requires.txt
SigProfilerExtractor.egg-info/top_level.txt
SigProfilerExtractor/controllers/cli_controller.py
SigProfilerExtractor/data/CNVInput/Battenberg_test.tsv
SigProfilerExtractor/data/CSVInput/csv_example.csv
SigProfilerExtractor/data/MatObjInput/21_breast_WGS_substitutions.mat
SigProfilerExtractor/data/ReferenceFiles/CNV_features.tsv
SigProfilerExtractor/data/ReferenceFiles/CN_classes_dictionary.txt
SigProfilerExtractor/data/TextInput/Samples_CNV.txt
SigProfilerExtractor/data/TextInput/Samples_DBS.txt
SigProfilerExtractor/data/TextInput/Samples_ID.txt
SigProfilerExtractor/data/TextInput/Samples_SBS.txt
SigProfilerExtractor/data/TextInput/Samples_SV.txt
SigProfilerExtractor/data/VCFInput/PD3851a.vcf
SigProfilerExtractor/data/VCFInput/PD3890a.vcf
SigProfilerExtractor/data/VCFInput/PD3904a.vcf
SigProfilerExtractor/data/VCFInput/PD3905a.vcf
SigProfilerExtractor/data/VCFInput/PD3945a.vcf
docs/1. Installation.md
docs/2. Quick Start Example.md
docs/3. Using the Tool - Input.md
docs/4. Using the Tool - Output.md
docs/5. Output - All Solutions.md
docs/6. Output - Suggested Solution.md
docs/home.md
docs/index.md
docs/assets/images/osf/4hnaj.png
docs/assets/images/osf/5f8ep.png
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docs/assets/images/osf/zu6sm.png
docs/assets/stylesheets/extra.css
wikies/CLI-Usage.md
wikies/Citation.md
wikies/Home.md
wikies/Installation.md
wikies/Output.md
wikies/Python-API.md
wikies/_Sidebar.md