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

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

## 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