.gitignore
.pre-commit-config.yaml
.readthedocs.yml
LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/black.yml
.github/workflows/publish.yml
.github/workflows/tests.yml
crema/__init__.py
crema/confidence.py
crema/crema.py
crema/dataset.py
crema/params.py
crema/qvalues.py
crema/utils.py
crema/parsers/__init__.py
crema/parsers/comet.py
crema/parsers/msamanda.py
crema/parsers/msfragger.py
crema/parsers/msgf.py
crema/parsers/mztab.py
crema/parsers/pepxml.py
crema/parsers/tide.py
crema/parsers/txt.py
crema/writers/__init__.py
crema/writers/txt.py
crema_ms.egg-info/PKG-INFO
crema_ms.egg-info/SOURCES.txt
crema_ms.egg-info/dependency_links.txt
crema_ms.egg-info/entry_points.txt
crema_ms.egg-info/requires.txt
crema_ms.egg-info/top_level.txt
data/MSV000085729.mzTab
data/example_psms_decoy.txt
data/example_psms_target.txt
data/msfragger.pepxml
data/tide-search.pep.xml
docs/CHANGELOG.md
docs/Makefile
docs/cli.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/_static/crema_logo_caramel_light.png
docs/_static/custom.css
docs/api/confidence.rst
docs/api/dataset.rst
docs/api/functions.rst
docs/api/index.rst
static/crema_logo.svg
tests/__init__.py
tests/conftest.py
tests/system_tests/__init__.py
tests/system_tests/test_cli.py
tests/system_tests/test_crux_tdc.py
tests/unit_tests/__init__.py
tests/unit_tests/test_confidence.py
tests/unit_tests/test_dataset.py
tests/unit_tests/test_parsers.py
tests/unit_tests/test_qvalues.py