.gitignore
AUDIT.md
CHANGELOG.md
CITATION.cff
CLAUDE.md
DATA_SOURCES.md
LICENSE
MANIFEST.in
Makefile
PLOTTING_REVIEW.md
README.md
RELEASE_CHECKLIST.md
ROADMAP.md
deploy.sh
pyproject.toml
pytest.ini
run_tests.py
pymaftools/__init__.py
pymaftools/_version.py
pymaftools/datasets.py
pymaftools/llm.py
pymaftools.egg-info/PKG-INFO
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pymaftools/core/Clustering.py
pymaftools/core/Cohort.py
pymaftools/core/CopyNumberVariationTable.py
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pymaftools/core/MAF.py
pymaftools/core/PairwiseMatrix.py
pymaftools/core/PivotTable.py
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pymaftools/core/variant_groups.py
pymaftools/data/.gitkeep
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pymaftools/data/ensembl_gene_sizes.tsv
pymaftools/data/example_multisample.maf
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pymaftools/data/example_tcga_lung_mutation_grouped.h5
pymaftools/data/protein_domains.csv
pymaftools/io/__init__.py
pymaftools/io/tcga_readers.py
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pymaftools/plot/OncoPlot.py
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pymaftools/plot/Track.py
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