LICENSE
MANIFEST.in
README.md
setup.py
.streamlit/config.toml
docs/CONDA_ENVIRONMENTS.md
docs/MIGRATION_GUIDE_v2.1_to_v2.2.md
docs/MODULE_10_Biomarker Discovery.md
docs/MODULE_1_Quick Quantification.md
docs/MODULE_2_Quality Assessment & Outlier Detection.md
docs/MODULE_3_Data Profiling.md
docs/MODULE_3_QUICK_REFERENCE.md
docs/MODULE_4_Pipeline Recommender and Selection.md
docs/MODULE_7_DE Import.md
docs/MODULE_8_Parameter Optimization.md
docs/MODULE_9_Ensemble Analysis.md
docs/RAPTOR_API_DOCUMENTATION.md
docs/RAPTOR_QUICK_REFERENCE.md
docs/RAPTOR_USER_GUIDE.md
examples/01_quick_count.py
examples/02_quality_assessment.py
examples/03_data_profiler.py
examples/04_recommender.py
examples/05_production_pipeline.py
examples/07_DE_Import.py
examples/08_Parameter_Optimization.py
examples/09_Ensemble_Analysis.py
examples/10_qc_scenarios.py
examples/11_recommender_scenarios.py
examples/README.md
examples/example_biomarker_discovery.py
raptor/__init__.py
raptor/cli.py
raptor/de_import.py
raptor/ensemble.py
raptor/launch_dashboard.py
raptor/ml_recommender.py
raptor/parameter_optimization.py
raptor/profiler.py
raptor/quality_assessment.py
raptor/recommender.py
raptor/simulation.py
raptor/synthetic_benchmarks.py
raptor/test_validation.py
raptor/biomarker_discovery/__init__.py
raptor/biomarker_discovery/clinical_metrics.py
raptor/biomarker_discovery/core.py
raptor/biomarker_discovery/direction_patterns.py
raptor/biomarker_discovery/enhanced.py
raptor/biomarker_discovery/intent.py
raptor/biomarker_discovery/ratio_biomarkers.py
raptor/biomarker_discovery/signature_score.py
raptor/biomarker_discovery/univariate_de.py
raptor/dashboard/__init__.py
raptor/dashboard/app.py
raptor/dashboard/assets/__init__.py
raptor/dashboard/assets/styles/Slide2.PNG
raptor/dashboard/assets/styles/__init__.py
raptor/dashboard/assets/styles/custom_styles.css
raptor/dashboard/assets/styles/style_loader.py
raptor/dashboard/components/__init__.py
raptor/dashboard/components/sidebar.py
raptor/dashboard/pages/01_📡_Data_Acquisition.py
raptor/dashboard/pages/02_✅_Quality.py
raptor/dashboard/pages/03__📊_Profiler.py
raptor/dashboard/pages/04_🤖_Recommender.py
raptor/dashboard/pages/05_📥_Import_DE.py
raptor/dashboard/pages/06_⚙️_Optimization.py
raptor/dashboard/pages/07_🔬_Ensemble.py
raptor/dashboard/pages/08_🧬_Biomarker_Discovery.py
raptor/dashboard/pages/09_📋_Reports.py
raptor/dashboard/pages/10_⚙️_Settings.py
raptor/dashboard/pages/11_📊_Visualization.py
raptor/dashboard/pages/__init__.py
raptor/dashboard/utils/__init__.py
raptor/external_modules/__init__.py
raptor/external_modules/acquisition/__init__.py
raptor/external_modules/acquisition/arrayexpress.py
raptor/external_modules/acquisition/base.py
raptor/external_modules/acquisition/cache.py
raptor/external_modules/acquisition/catalog.py
raptor/external_modules/acquisition/datasets.py
raptor/external_modules/acquisition/gene_mapping.py
raptor/external_modules/acquisition/geo.py
raptor/external_modules/acquisition/pooling.py
raptor/external_modules/acquisition/sra.py
raptor/external_modules/acquisition/tcga.py
raptor/external_modules/module6_de_analysis/README.md
raptor/external_modules/module6_de_analysis/__init__.py
raptor/external_modules/module6_de_analysis/recomendation.txt
raptor/external_modules/module6_de_analysis/documentation/MODULE6_COMPLETION_SUMMARY.md
raptor/external_modules/module6_de_analysis/documentation/MODULE6_R_SCRIPTS_ANALYSIS.md
raptor/external_modules/module6_de_analysis/python_wrappers/__init__.py
raptor/external_modules/module6_de_analysis/python_wrappers/run_de_analysis.py
raptor/external_modules/module6_de_analysis/r_scripts/install_packages.R
raptor/external_modules/module6_de_analysis/r_scripts/run_deseq2.R
raptor/external_modules/module6_de_analysis/r_scripts/run_edger.R
raptor/external_modules/module6_de_analysis/r_scripts/run_limma.R
raptor/pipelines/__init__.py
raptor/pipelines/base.py
raptor/pipelines/hisat2_featurecounts/__init__.py
raptor/pipelines/hisat2_featurecounts/config.yaml
raptor/pipelines/hisat2_featurecounts/pipeline.py
raptor/pipelines/hisat2_featurecounts/run_hisat2_featurecounts.sh
raptor/pipelines/kallisto/__init__.py
raptor/pipelines/kallisto/config.yaml
raptor/pipelines/kallisto/pipeline.py
raptor/pipelines/kallisto/run_kallisto.sh
raptor/pipelines/quick_kallisto/README.md
raptor/pipelines/quick_kallisto/__init__.py
raptor/pipelines/quick_kallisto/combine_counts.py
raptor/pipelines/quick_kallisto/config.yaml
raptor/pipelines/quick_kallisto/detect_samples.py
raptor/pipelines/quick_kallisto/generate_report.py
raptor/pipelines/quick_kallisto/kallisto_quant.py
raptor/pipelines/quick_kallisto/run_quick.sh
raptor/pipelines/quick_salmon/__init__.py
raptor/pipelines/quick_salmon/combine_counts.py
raptor/pipelines/quick_salmon/config.yaml
raptor/pipelines/quick_salmon/detect_samples.py
raptor/pipelines/quick_salmon/generate_report.py
raptor/pipelines/quick_salmon/run_quick.sh
raptor/pipelines/quick_salmon/salmon_quant.py
raptor/pipelines/salmon/__init__.py
raptor/pipelines/salmon/config.yaml
raptor/pipelines/salmon/pipeline.py
raptor/pipelines/salmon/run_salmon.sh
raptor/pipelines/star_featurecounts/__init__.py
raptor/pipelines/star_featurecounts/config.yaml
raptor/pipelines/star_featurecounts/pipeline.py
raptor/pipelines/star_featurecounts/run_featurecounts.sh
raptor/pipelines/star_featurecounts/run_star.sh
raptor/pipelines/star_rsem/__init__.py
raptor/pipelines/star_rsem/config.yaml
raptor/pipelines/star_rsem/pipeline.py
raptor/pipelines/star_rsem/run_rsem.sh
raptor/pipelines/star_salmon/STAR_SALMON_COMPLETE_SUMMARY.md
raptor/pipelines/star_salmon/__init__.py
raptor/pipelines/star_salmon/config.yaml
raptor/pipelines/star_salmon/pipeline.py
raptor/utils/__init__.py
raptor/utils/errors.py
raptor/utils/sample_sheet.py
raptor/utils/validation.py
raptor_rnaseq.egg-info/PKG-INFO
raptor_rnaseq.egg-info/SOURCES.txt
raptor_rnaseq.egg-info/dependency_links.txt
raptor_rnaseq.egg-info/entry_points.txt
raptor_rnaseq.egg-info/not-zip-safe
raptor_rnaseq.egg-info/requires.txt
raptor_rnaseq.egg-info/top_level.txt
templates/sample_sheet_paired.csv
templates/sample_sheet_single.csv
tests/__init__.py
tests/conftest.py
tests/generate_edge_case_data.py
tests/generate_realistic_test_data.py
tests/test_acquisition.py
tests/test_base_pipeline.py
tests/test_biomarker_best_classifier_selection.py
tests/test_biomarker_clinical_metrics_oof.py
tests/test_biomarker_discovery.py
tests/test_biomarker_intent.py
tests/test_biomarker_m4_calibration.py
tests/test_biomarker_optimism_diagnostic_m2.py
tests/test_biomarker_pipeline_cv.py
tests/test_biomarker_rfe_ranking.py
tests/test_cli_comprehensive.py
tests/test_cli_kneedle.py
tests/test_clinical_metrics.py
tests/test_combine_counts.py
tests/test_dashboard_panel_stability.py
tests/test_de_import.py
tests/test_detect_samples.py
tests/test_direction_patterns.py
tests/test_enhanced.py
tests/test_ensemble.py
tests/test_generate_report.py
tests/test_m10_cli_scenarios.py
tests/test_panel_size_kneedle.py
tests/test_parameter_optimization.py
tests/test_pipelines.py
tests/test_pipelines_cli.py
tests/test_profiler.py
tests/test_quality_assessment.py
tests/test_quant_pipelines.py
tests/test_ratio_biomarkers.py
tests/test_recommender.py
tests/test_signature_score.py