Differential Drug Sensitivity Analysis for Two-Condition High-Throughput Screens

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Documentation for package ‘diffHTS’ version 0.1.0

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

Help Pages

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
calculate_qc_metrics	Plate-level quality-control metrics for high-throughput screens
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
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
coef.dsr_4pl	Fit a four-parameter logistic dose-response model
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
fitted.dsr_4pl	Fit a four-parameter logistic dose-response model
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
plate_layout_1536	Standard microplate coordinate map
plate_layout_384	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
predict.dsr_4pl	Fit a four-parameter logistic dose-response model
print.dsr_4pl	Fit a four-parameter logistic dose-response model
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
residuals.dsr_4pl	Fit a four-parameter logistic dose-response model
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