.calculate_control_collinearity
                        Calculate exact fixed-model diagnostics for a
                        control reference matrix.
.calculate_control_uds_use
                        Calculate empirical USE and matched fixed-model
                        SIF ratios.
.calculate_fixed_collinearity_vif_magnitude_sif
                        Calculate exact VIF magnitude and SIF values
                        for one fixed effective model.
adjust_control_reference
                        Adjust a completed control reference matrix
build_reference_matrix
                        Build a Reference Matrix from Single-Color
                        Controls
calc_residuals          Calculate unmixing residuals
calculate_af_repertoire_qc_metrics
                        Calculate deterministic AF-repertoire
                        diagnostics
calculate_control_qc_metrics
                        Calculate deterministic event-level SCC quality
                        metrics
calculate_cosine_similarity_matrix
                        Calculate a cosine-similarity matrix
calculate_nps           Calculate the negative-tail MAD proxy
                        (historically NPS)
calculate_similarity_matrix
                        Calculate a cosine-similarity matrix (legacy
                        name)
calculate_unstained_robust_spread
                        Calculate robust spread for unmixed
                        unstained-control coefficients
check_for_updates       Check for and install Spectreasy updates
collect_control_report_bundle
                        Collect a modular control QC report bundle
collect_control_report_data
                        Collect control QC report data
collect_sample_report_bundle
                        Collect a modular sample QC report bundle
collect_sample_report_data
                        Collect sample QC report data
control_qc_modules_default
                        Default control QC modules
control_qc_reports_default
                        Default control QC reports
create_control_file     Create spectreasy Control File
derive_unmixing_matrix
                        Derive Unmixing Matrix from Reference Matrix
export_qc_report_pdf    Export an existing Spectreasy HTML QC report to
                        PDF
extract_control_spectra
                        Automatically Gate and Extract Control Spectra
gate_controls           Gate Single-Color Controls Interactively
get_control_spectra     Get Previously Extracted Control Spectra
get_fluorophore_patterns
                        Get Standard Fluorophore Filename Patterns
get_sorted_detectors    Get Sorted Detectors by Laser and Wavelength
inspect_fcs_provenance
                        Inspect scientific provenance embedded in FCS
                        files
inspect_spectreasy_provenance
                        Inspect a portable provenance envelope produced
                        by Spectreasy
install_qc_dependencies
                        Ensure the CompensAID QC dependency
launch                  Launch the Spectreasy GUI
plot_compensaid_matrix
                        Plot a directional CompensAID SSI matrix
plot_compensaid_pair    Plot one CompensAID directional marker pair
plot_control_compensaid_matrix
                        Plot a control directional SSI matrix
plot_cosine_similarity_matrix
                        Plot a cosine-similarity matrix
plot_nps                Plot historical negative-tail spread
plot_sample_rms_residuals
                        Plot Overall Detector Reconstruction Error
                        Across Samples
plot_similarity_matrix
                        Plot a cosine-similarity matrix (legacy name)
plot_spectra            Plot Spectral Overlays
plot_unmixing_matrix    Plot Unmixing Matrix
plot_unmixing_scatter_matrix
                        Plot NxN Unmixing Scatter Matrix
qc_controls             Generate modular control QC reports
qc_samples              Generate modular sample QC reports
read_control_extraction
                        Read Extracted Control Spectra for Direct R
                        Unmixing
read_control_reference
                        Read a completed control reference
read_sample_run_manifest
                        Read a persisted sample-run manifest.
render_qc_html_report   Render a Spectreasy QC report object as HTML
sample_qc_modules_default
                        Default sample QC modules
sample_qc_reports_default
                        Default sample QC reports
save_unmixing_matrix    Save Unmixing Matrix to CSV
spectreasy_capabilities
                        Report stable behavioral capabilities
spectreasy_example_data
                        Download and cache the spectreasy example FCS
                        files
spectreasy_gui_runtime
                        Create a host-composable Spectreasy GUI runtime
                        session
spectreasy_native_map_data_to_codes_cpp
                        Map data onto a trained SOM codebook
                        (OpenMP-accelerated)
spectreasy_native_som_train_batch_cpp
                        Train a Self-Organizing Map with batch updates
                        (OpenMP-accelerated)
supported_cytometers    Supported Cytometers
unmix_controls          Unmix Single-Color Controls
unmix_samples           Unmix Experimental Samples
validate_control_file_mapping
                        Validate SCC Control Mapping Before Unmixing
validate_sample_run     Validate a persisted sample-run manifest and
                        its output provenance.
verify_spectreasy_provenance
                        Verify portable provenance checksums for
                        Spectreasy artifacts
