Leakage-Aware Discovery of Small Biomarker Panels

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Documentation for package ‘detectPanel’ version 0.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

detectPanel-package	Leakage-Aware Discovery of Small Biomarker Panels
confusion_metrics	Compute Confusion-Matrix Metrics
detectPanel	Discover, Validate, and Refit a Biomarker Panel
discover_panel	Discover, Validate, and Refit a Biomarker Panel
evaluate_markers	Score and Preselect Candidate Biomarkers
exclude_features	Validate, Filter, and Transform Assay Data
export_results	Export detectPanel Results
fit_panel	Fit and Predict with a Biomarker Panel
flag_pca_outliers	Flag Potential PCA Outliers Without Deleting Samples
make_repeated_stratified_splits	Shared Resampling Splits and Exhaustive Panel Search
nested_validate_panels	Nested Validation of Biomarker Panel Discovery
plot.detectPanel_nested	Nested Validation of Biomarker Panel Discovery
plot.detectPanel_result	Discover, Validate, and Refit a Biomarker Panel
plot_marker_expression	Diagnostic Plotting Helpers
plot_marker_roc	Diagnostic Plotting Helpers
plot_panel_heatmap	Diagnostic Plotting Helpers
plot_volcano	Diagnostic Plotting Helpers
predict.detectPanel_fit	Fit and Predict with a Biomarker Panel
predict.detectPanel_result	Predict samples using a fitted detectPanel result
preselect_markers	Score and Preselect Candidate Biomarkers
print.detectPanel_fit	Fit and Predict with a Biomarker Panel
print.detectPanel_nested	Nested Validation of Biomarker Panel Discovery
print.detectPanel_result	Discover, Validate, and Refit a Biomarker Panel
print.detectPanel_search	Shared Resampling Splits and Exhaustive Panel Search
run_deseq2	Optional DESeq2 Differential-Expression Adapter
score_detectability	Score and Preselect Candidate Biomarkers
search_panels	Shared Resampling Splits and Exhaustive Panel Search
summary.detectPanel_fit	Fit and Predict with a Biomarker Panel
summary.detectPanel_nested	Nested Validation of Biomarker Panel Discovery
summary.detectPanel_result	Discover, Validate, and Refit a Biomarker Panel
transform_assay	Validate, Filter, and Transform Assay Data
validate_assay_data	Validate, Filter, and Transform Assay Data