.gitignore
LICENSE.md
README.md
pyfraglib.yml
pyproject.toml
setup.py
configs/gmm_1.json
configs/gmm_2.json
configs/gmm_3.json
configs/simulation_basic.json
configs/simulation_cancer_progression.json
configs/simulation_tissue_mixture.json
docs/Makefile
docs/pyfraglib_documentation.pdf
docs/requirements.txt
docs/imgs/api_classes.dot
docs/imgs/api_classes.png
docs/imgs/cfdna_cleavage_biology.dot
docs/imgs/cfdna_cleavage_biology.png
docs/imgs/nf_pipeline.dot
docs/imgs/nf_pipeline.png
docs/imgs/pyfraglib_logo.jpg
docs/imgs/pyfraglib_logo.png
docs/imgs/pyfraglib_logo_old.jpg
docs/imgs/simulation_architecture.dot
docs/imgs/simulation_architecture.png
docs/imgs/simulation_architecture_simplified.dot
docs/imgs/simulation_architecture_simplified.png
docs/imgs/workflow.dot
docs/imgs/workflow.png
docs/source/changelog.rst
docs/source/conf.py
docs/source/contributing.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/quickstart.rst
docs/source/_static/custom.css
docs/source/_templates/autosummary/class.rst
docs/source/api/index.rst
docs/source/cli/extract.rst
docs/source/cli/index.rst
docs/source/cli/lengths.rst
docs/source/cli/scores.rst
docs/source/cli/scripts.rst
docs/source/cli/simulate.rst
docs/source/cli/stats.rst
docs/source/simulation/index.rst
notebooks/gmm_demo.py
notebooks/pcnsl_gmm.py
notebooks/pcnsl_visualize_vcf.py
notebooks/pcnsl_visualize_wps_MYD88.py
notebooks/pcnsl_wpr_predictor.py
notebooks/pcnsl_wps_predictor.py
notebooks/start_marimo_server.sh
pyfraglib/__init__.py
pyfraglib/core.py
pyfraglib/fragfile.py
pyfraglib/fragment.py
pyfraglib/lengths.py
pyfraglib/math.py
pyfraglib/py.typed
pyfraglib/scores.py
pyfraglib/stats.py
pyfraglib.egg-info/PKG-INFO
pyfraglib.egg-info/SOURCES.txt
pyfraglib.egg-info/dependency_links.txt
pyfraglib.egg-info/requires.txt
pyfraglib.egg-info/top_level.txt
pyfraglib/simulator/__init__.py
pyfraglib/simulator/fragment_simulator.py
pyfraglib/simulator/tissue_mixture_simulator.py
scripts/__init__.py
scripts/differential_end_motifs.py
scripts/differential_wps.py
scripts/download_tss_annos.py
scripts/extract_mutated_reads.py
scripts/learn_nuclease_params.py
scripts/nmf_fragment_lengths.py
scripts/pyfrag.py
scripts/txt_to_vcf.py
tests/__init__.py
tests/test_core.py
tests/test_differential_wps.py
tests/test_fixtures.py
tests/test_fragfile.py
tests/test_fragment.py
tests/test_math.py
tests/test_nmf.py
tests/test_runner.py
tests/test_scores.py
tools/annotate.sh
tools/build_docs.sh
tools/clean.sh
tools/dev_install.sh
tools/example.config
tools/example_sample_sheet.tsv
tools/pipeline.nf
tools/publish.sh
tools/workflow.sh