LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
src/rpbp/__init__.py
src/rpbp/defaults.py
src/rpbp/run_all_rpbp_instances.py
src/rpbp/run_rpbp_pipeline.py
src/rpbp.egg-info/PKG-INFO
src/rpbp.egg-info/SOURCES.txt
src/rpbp.egg-info/dependency_links.txt
src/rpbp.egg-info/entry_points.txt
src/rpbp.egg-info/requires.txt
src/rpbp.egg-info/top_level.txt
src/rpbp/analysis/__init__.py
src/rpbp/analysis/profile_construction/__init__.py
src/rpbp/analysis/profile_construction/collect_read_length_orf_profiles.py
src/rpbp/analysis/profile_construction/create_read_length_orf_profiles.py
src/rpbp/analysis/profile_construction/get_all_read_filtering_counts.py
src/rpbp/analysis/profile_construction/summarize_rpbp_profile_construction.py
src/rpbp/analysis/profile_construction/visualize_metagene_profile_bayes_factor.py
src/rpbp/analysis/profile_construction/dashboard/__init__.py
src/rpbp/analysis/profile_construction/dashboard/controls.py
src/rpbp/analysis/profile_construction/dashboard/rpbp_profile_construction_dashboard.py
src/rpbp/analysis/proteomics/__init__.py
src/rpbp/analysis/proteomics/filter_nonunique_peptide_matches.py
src/rpbp/analysis/proteomics/get_all_orf_peptide_matches.py
src/rpbp/analysis/proteomics/get_orf_peptide_matches.py
src/rpbp/analysis/rpbp_predictions/__init__.py
src/rpbp/analysis/rpbp_predictions/summarize_rpbp_predictions.py
src/rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py
src/rpbp/analysis/rpbp_predictions/dashboard/__init__.py
src/rpbp/analysis/rpbp_predictions/dashboard/rpbp_predictions_dashboard.py
src/rpbp/analysis/rpbp_predictions/dashboard/assets/logo-rpbp.png
src/rpbp/analysis/rpbp_predictions/dashboard/assets/schematic.png
src/rpbp/analysis/rpbp_predictions/dashboard/assets/style.css
src/rpbp/models/__init__.py
src/rpbp/models/nonperiodic/__init__.py
src/rpbp/models/nonperiodic/no-periodicity.stan
src/rpbp/models/nonperiodic/start-high-high-low.stan
src/rpbp/models/nonperiodic/start-high-low-high.stan
src/rpbp/models/periodic/__init__.py
src/rpbp/models/periodic/start-high-low-low.stan
src/rpbp/models/translated/__init__.py
src/rpbp/models/translated/periodic-gaussian-mixture.stan
src/rpbp/models/untranslated/__init__.py
src/rpbp/models/untranslated/gaussian-naive-bayes.stan
src/rpbp/orf_profile_construction/__init__.py
src/rpbp/orf_profile_construction/create_base_genome_profile.py
src/rpbp/orf_profile_construction/create_orf_profiles.py
src/rpbp/orf_profile_construction/estimate_metagene_profile_bayes_factors.py
src/rpbp/orf_profile_construction/extract_metagene_profiles.py
src/rpbp/orf_profile_construction/extract_orf_profiles.py
src/rpbp/orf_profile_construction/select_periodic_offsets.py
src/rpbp/reference_preprocessing/__init__.py
src/rpbp/reference_preprocessing/extract_orf_coordinates.py
src/rpbp/reference_preprocessing/label_orfs.py
src/rpbp/reference_preprocessing/prepare_rpbp_genome.py
src/rpbp/ribo_utils/__init__.py
src/rpbp/ribo_utils/compile_rpbp_models.py
src/rpbp/ribo_utils/filenames.py
src/rpbp/ribo_utils/utils.py
src/rpbp/translation_prediction/__init__.py
src/rpbp/translation_prediction/estimate_orf_bayes_factors.py
src/rpbp/translation_prediction/merge_replicate_orf_profiles.py
src/rpbp/translation_prediction/predict_translated_orfs.py
src/rpbp/translation_prediction/select_final_prediction_set.py