├── .gitattributes ├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── config_files ├── FP18.yaml ├── SQC.yaml ├── SQC_varied_all.yaml └── example_sqc_67_95_varied.yaml ├── dart_id.sh ├── dart_id ├── __init__.py ├── align.py ├── collator.py ├── config │ ├── defaults.yaml │ └── schema.yaml ├── converter.py ├── exceptions.py ├── fido │ ├── BayesianNetwork.py │ ├── BinomialHeap.py │ ├── Fido MIT license.txt │ ├── GraphUtilities.py │ ├── Utilities.py │ └── __init__.py ├── fido_cpp_interface.py ├── helper.py ├── models.py ├── models │ ├── fit_RT3e.stan │ ├── fit_RT3e │ │ ├── debian │ │ │ └── fit_RT3e │ │ ├── linux_generic │ │ │ └── fit_RT3e │ │ ├── mac │ │ │ └── fit_RT3e │ │ ├── rhel │ │ │ └── fit_RT3e │ │ └── windows │ │ │ ├── fit_RT3e.exe │ │ │ └── libwinpthread-1.dll │ └── fit_RT_linear.stan ├── notebooks │ └── dart_id_report.ipynb ├── report.py ├── update.py └── version.py ├── docs ├── .gitignore ├── .stylelintrc.json ├── 404.html ├── CNAME ├── Gemfile ├── LICENSE.txt ├── Rakefile ├── _config.yml ├── _includes │ ├── head.html │ └── nav.html ├── _layouts │ ├── about.html │ ├── default.html │ ├── home.html │ ├── page.html │ └── post.html ├── _sass │ ├── base.scss │ ├── buttons.scss │ ├── code.scss │ ├── color_schemes │ │ └── dark.scss │ ├── content.scss │ ├── custom │ │ └── custom.scss │ ├── labels.scss │ ├── layout.scss │ ├── navigation.scss │ ├── search.scss │ ├── support │ │ ├── _functions.scss │ │ ├── _variables.scss │ │ ├── mixins │ │ │ ├── _buttons.scss │ │ │ ├── _layout.scss │ │ │ ├── _typography.scss │ │ │ └── mixins.scss │ │ └── support.scss │ ├── tables.scss │ ├── typography.scss │ ├── utilities │ │ ├── _colors.scss │ │ ├── _layout.scss │ │ ├── _lists.scss │ │ ├── _spacing.scss │ │ ├── _typography.scss │ │ └── utilities.scss │ └── vendor │ │ └── normalize.scss │ │ ├── README.md │ │ ├── normalize.scss │ │ └── package.json ├── assets │ ├── css │ │ ├── dark-mode-preview.scss │ │ └── just-the-docs.scss │ ├── images │ │ ├── alignment_103_180413S_X_FP18I.png │ │ ├── fold_change_ids.png │ │ ├── just-the-docs.png │ │ ├── pep_new_scatterplot.png │ │ ├── residual_boxplot.png │ │ └── search.svg │ └── js │ │ ├── just-the-docs.js │ │ ├── search-data.json │ │ └── vendor │ │ ├── MathJax.js │ │ └── lunr.min.js ├── bin │ └── just-the-docs ├── build_search_index.sh ├── docs │ ├── column_descs.md │ ├── config_file.md │ ├── debug_alignment.md │ ├── figures.md │ ├── input_format │ │ ├── example_input_file.md │ │ └── input_format.md │ ├── installation │ │ ├── from_source.md │ │ ├── installation.md │ │ ├── linux.md │ │ ├── osx.md │ │ └── windows.md │ ├── stan_model.md │ └── video.md ├── favicon.ico ├── index.md ├── just-the-docs.gemspec ├── lib │ └── tasks │ │ └── search.rake ├── mass-spec │ └── methods.md ├── package.json └── serve.sh ├── environment.yml ├── example ├── config.yaml ├── config_annotated.yaml └── config_sequest.yaml ├── requirements.txt ├── set_environment.sh ├── setup.cfg └── setup.py /.gitattributes: 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