.gitignore
.pre-commit-config.yaml
.readthedocs.yml
CHANGELOG.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
Makefile
README.md
codecov.yml
pyproject.toml
setup.py
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/black.yml
.github/workflows/publish.yml
.github/workflows/tests.yml
data/README.md
data/human_sp_td.fasta
data/msfragger.pepXML
data/percolator.peptides.txt
data/percolator.proteins.txt
data/percolator.psms.txt
data/phospho_rep1.pin
data/scope2_FP97AA.pin
data/scope2_FP97AB.pin
data/scope2_FP97AC.pin
docs/Makefile
docs/make.bat
docs/source/CHANGELOG.md
docs/source/CODE_OF_CONDUCT.md
docs/source/cli.rst
docs/source/conf.py
docs/source/contributing.rst
docs/source/faq.rst
docs/source/index.rst
docs/source/_static/custom.css
docs/source/_static/edit.png
docs/source/_static/mokapot_logo_light.png
docs/source/api/confidence.rst
docs/source/api/dataset.rst
docs/source/api/functions.rst
docs/source/api/index.rst
docs/source/api/model.rst
docs/source/vignettes/basic_python_api.ipynb
docs/source/vignettes/index.rst
docs/source/vignettes/joint_models.ipynb
docs/source/vignettes/percolator_comparison.ipynb
mokapot/__init__.py
mokapot/brew.py
mokapot/confidence.py
mokapot/config.py
mokapot/dataset.py
mokapot/model.py
mokapot/mokapot.py
mokapot/peptides.py
mokapot/picked_protein.py
mokapot/proteins.py
mokapot/qvalues.py
mokapot/utils.py
mokapot.egg-info/PKG-INFO
mokapot.egg-info/SOURCES.txt
mokapot.egg-info/dependency_links.txt
mokapot.egg-info/entry_points.txt
mokapot.egg-info/requires.txt
mokapot.egg-info/top_level.txt
mokapot/parsers/__init__.py
mokapot/parsers/pepxml.py
mokapot/parsers/pin.py
static/mokapot_logo_dark.svg
tests/__init__.py
tests/fixtures.py
tests/system_tests/test_cli.py
tests/system_tests/test_system.py
tests/unit_tests/__init__.py
tests/unit_tests/test_brew.py
tests/unit_tests/test_confidence.py
tests/unit_tests/test_dataset.py
tests/unit_tests/test_model.py
tests/unit_tests/test_mokapot.py
tests/unit_tests/test_parser_pepxml.py
tests/unit_tests/test_parser_pin.py
tests/unit_tests/test_peptides.py
tests/unit_tests/test_picked_protein.py
tests/unit_tests/test_proteins.py
tests/unit_tests/test_qvalues.py
tests/unit_tests/test_utils.py