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Orangepipeline merged - #96
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…; remove cancer_type from lung configuration
…ions for stomach, rectal, and lung configurations
…ions for lung, rectal, and stomach configurations
…lass distribution
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Keep oversampled GDC results/config as *_oversample and restore originals to 78101d3 to avoid merge conflicts with prostate/GSE269244. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Stale copy from breast-orangepipline (520c9cf); conflicts with breast branch's version. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Resolve conflicts with rectal_plan_A_results_SMOTE (= master) versions: lung/training_param.json, rectal/training_param.json, notebooks/orange_pipeline_orchestrator_planA.ipynb Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Resolve 97 add/add conflicts by keeping the newer version: - orangepipeline-merged: lung/result/** (44), config/lung.toml, config/prostate.toml, config/rectal.toml, config/stomach.json, config/stomach.toml, notebooks/utils/painter.py - clean_up: stomach/planA/joined/**, breast/planA/joined/**, prostate/planA/joined/** (44), config/prostate.json, config/prostate_plan_A.toml, prostate/training_param.json Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…st packages and improving renv caching mechanism
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This pull request introduces new data files and updates existing scripts and outputs to support analysis of methylation data for both TCGA and GSE66313 breast cancer datasets. It updates input data paths and output filenames in the main R script, and adds feature selection results for several machine learning models in both CSV and JSON formats.
Key changes include:
Data Processing Updates
R-scripts/parse.Rto use thedata/TCGA_COAD_READdataset and reflect this in the output CSVs.New Data and Results Files
dbeta_TSS_0.33.csvfiles for bothbreast/planA/GSE66313/split60train/section_2/andbreast/planA/TCGA_BRCA_20250119/split60train/section_2/, containing differentially methylated positions and associated gene/feature information. [1] [2]Feature Selection Outputs
selected_feature.txtfiles for both datasets, listing the incremental feature sets selected by SVM, DecisionTree, RandomForest, and XGBoost models. [1] [2]selected_features.jsonfile for GSE66313, providing a structured summary of selected features for each model.