annotate_hit_info       Annotate hits with compound metadata
apply_plate_layout      Stamp a plate-map layout onto measured readings
baseline_subtract       Subtract the blank background signal from a
                        plate
build_auc_matrix        Build a compound-by-sample AUC matrix
calc_cv                 Control coefficient of variation per plate
calc_drc_auc            Area under the dose-response curve
calc_plate_qc           Comprehensive per-plate quality assessment
calc_replicate_correlation
                        Pairwise replicate correlation between plates
calc_replicate_cv       Replicate coefficient of variation per compound
calc_robust_z_prime     Robust Z'-factor per plate
calc_sb_ratio           Signal-to-background ratio per plate
calc_sn_ratio           Signal-to-noise ratio per plate
calc_ssmd               SSMD per plate (strictly standardised mean
                        difference)
calc_well_zscore        Per-well standard and robust Z-scores
calc_z_factor           Z-factor per plate (sample-aware)
calc_z_prime            Compute per-plate Z' factors
calculate_qc_metrics    Plate-level quality-control metrics for
                        high-throughput screens
check_control_label     Validate control-well labelling
clean_compound_id       Standardise compound identifiers
clean_filename          Sanitise a string for use as a file name
cluster_auc_matrix      Hierarchically cluster an AUC matrix
compute_auc             Area under a four-parameter logistic
                        dose-response curve
compute_delta_auc       Differential (delta) AUC between two screening
                        conditions
convert_conc_log10      Convert concentrations to a log10 scale
detect_outlier_wells    Flag outlier wells by the IQR rule
export_hit_table        Export a hit summary table
extract_cluster_hit     Extract the most active compound cluster
extract_drc_params      Extract dose-response parameters
filter_bad_replicate    Drop compounds with poor replicate
                        reproducibility
filter_low_quality_curve
                        Drop low-quality dose-response curves
filter_valid_plates     Keep only plates that pass the Z' threshold
fit_4pl_curve           Fit four-parameter logistic curves per compound
fit_dose_response       Fit a four-parameter logistic dose-response
                        model
flag_qc_plates          Flag plates that fail quality-control
                        thresholds
four_pl                 Four-parameter logistic (4PL) dose-response
                        function
generate_hts_report     Generate an HTML screening report
hts_compound_meta       Example compound metadata
hts_dose_response       Example gradient dose-response secondary screen
hts_pal                 Colourblind-safe qualitative palette for
                        diffHTS
hts_plate_384           Example single 384-well screening plate
                        (realistic layout)
hts_primary_raw         Example single-concentration primary screen
                        (raw signals)
import_dose_response    Import gradient dose-response data
merge_plate_data        Combine normalised plates into one data set
norm_by_control         Normalise wells to plate controls
plate_layout            Standard microplate coordinate map
plot_auc_heatmap        AUC clustering heatmap
plot_batch_drc_overlay
                        Overlay multiple dose-response curves
plot_cluster_tree       Plot the compound clustering dendrogram
plot_condition_scatter
                        Scatter plot comparing two conditions or cell
                        lines
plot_control_scatter    Scatter plot of control readouts across plates
plot_cv_distribution    Histogram of replicate CV values
plot_delta_auc_heatmap
                        Heatmap of differential AUC across conditions
                        or cell lines
plot_dose_response_curves
                        Plot dose-response curves for two conditions
plot_hit_bar_count      Hit-count bar chart
plot_hit_stratify_bar   Stratified hit-count bar chart
plot_ic50_auc_cor       IC50 versus AUC scatter
plot_inhibition_hist    Histogram of compound inhibition on a plate
plot_plate_heatmap      Plate-layout heatmap of well readouts
plot_plate_heatmap_inhibition
                        Percent-inhibition plate heatmap
plot_plate_heatmap_raw
                        Raw-signal plate heatmap
plot_plate_qc           Visualise any plate quality-control metric
plot_primary_inhibition_rank
                        Ranked primary-activity curve
plot_primary_secondary_cor
                        Primary versus secondary activity correlation
plot_qc_boxplot         Quality-control boxplot of control wells across
                        plates
plot_qc_circular_heatmap
                        Circular heatmap of control readouts across
                        plates
plot_qc_metric_circular
                        Circular plot of a per-plate QC metric
plot_qc_metric_trend    Trend plot of a QC metric across plates
plot_replicate_scatter
                        Replicate scatter plot(s) with regression fit
                        and correlation
plot_sigma_hits         Distribution plot of sigma-based hits
plot_single_drc         Plot a single dose-response curve
rank_hit_compound       Rank and stratify hit compounds
read_hts_plate          Import a plate readout file into a standard HTS
                        object
read_plate_layout       Read a user-defined plate-map layout file
screen_delta_auc        Example differential-AUC hit table
screen_doseresponse     Example two-condition dose-response screen
screen_plate_layout     Example 96-well plate layout with well
                        positions
screen_plate_qc         Example per-plate quality-control summary
select_hits_cutoff      Select hits by an absolute cut-off across
                        conditions
select_hits_sigma       Select hits by a sigma (z-score) threshold
select_primary_hit      Select primary-screen hits
select_sigma_hits       Select primary-screen hits by distance from the
                        library distribution
summarize_plate_setup   Summarise how each plate in a run is set up
summarize_primary_hit   Summarise primary-screen hits
summarize_sigma_hits    Summarise sigma-based hits
theme_hts               Modern academic ggplot2 theme for diffHTS
                        figures
windows_to_linux_path   Convert a Windows path to a forward-slash path
