Package: diffHTS 0.1.0

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

A complete workflow for large-scale, two-condition high-throughput drug screening (HTS). It compares drug sensitivity between any two experimental conditions - for example irradiated versus non-irradiated cells, cancer versus normal cell lines, or treated versus untreated samples - across many plates and experiments. The package covers the full pipeline: control-based normalisation, plate-level quality-control metrics (Z-factor, Z-prime, signal-to-background, signal-to-noise and strictly standardised mean difference), replicate-consistency checks, four-parameter logistic dose-response fitting with area under the curve (AUC) estimation, differential (delta) AUC scoring with within-plate standardisation, cut-off and sigma-based hit selection, and publication-ready heatmap, scatter and quality-control visualisations.

Authors:Liang Tang [aut, cre]

diffHTS_0.1.0.tar.gz
diffHTS_0.1.0.zip(r-4.7-any)diffHTS_0.1.0.zip(r-4.6-any)diffHTS_0.1.0.zip(r-4.5-any)
diffHTS_0.1.0.tgz(r-4.6-any)diffHTS_0.1.0.tgz(r-4.5-any)
diffHTS_0.1.0.tar.gz(r-4.7-any)diffHTS_0.1.0.tar.gz(r-4.6-any)
diffHTS_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
diffHTS/json (API)

# Install 'diffHTS' in R:

install.packages('diffHTS', repos = c('https://kongjianyang.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

hts_compound_meta - Example compound metadata
hts_dose_response - Example gradient dose-response secondary screen
hts_plate_384 - Example single 384-well screening plate
hts_primary_raw - Example single-concentration primary screen
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

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 344 downloads 80 exports 29 dependencies

Last updated from:67aacbc050. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	181
source / vignettes	OK	241
linux-release	OK	169
macos-release	OK	158
macos-oldrel	OK	178
windows-devel	OK	144
windows-release	OK	94
windows-oldrel	OK	118
wasm-release	OK	140

Exports:annotate_hit_info apply_plate_layout baseline_subtract build_auc_matrix calc_cv calc_drc_auc calc_plate_qc calc_replicate_correlation calc_replicate_cv calc_robust_z_prime calc_sb_ratio calc_sn_ratio calc_ssmd calc_well_zscore calc_z_factor calc_z_prime calculate_qc_metrics check_control_label clean_compound_id clean_filename cluster_auc_matrix compute_auc compute_delta_auc convert_conc_log10 detect_outlier_wells export_hit_table extract_cluster_hit extract_drc_params filter_bad_replicate filter_low_quality_curve filter_valid_plates fit_4pl_curve fit_dose_response flag_qc_plates four_pl generate_hts_report hts_pal import_dose_response merge_plate_data norm_by_control plate_layout plate_layout_1536 plate_layout_384 plot_auc_heatmap plot_batch_drc_overlay plot_cluster_tree plot_condition_scatter plot_control_scatter plot_cv_distribution plot_delta_auc_heatmap plot_dose_response_curves plot_hit_bar_count plot_hit_stratify_bar plot_ic50_auc_cor plot_inhibition_hist plot_plate_heatmap plot_plate_heatmap_inhibition plot_plate_heatmap_raw plot_plate_qc plot_primary_inhibition_rank plot_primary_secondary_cor plot_qc_boxplot plot_qc_circular_heatmap plot_qc_metric_circular plot_qc_metric_trend plot_replicate_scatter plot_sigma_hits plot_single_drc rank_hit_compound read_hts_plate read_plate_layout select_hits_cutoff select_hits_sigma select_primary_hit select_sigma_hits summarize_plate_setup summarize_primary_hit summarize_sigma_hits theme_hts windows_to_linux_path

Dependencies:cli cpp11 dplyr farver generics ggplot2 glue gtable isoband labeling lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Analysing a two-condition drug screen with diffHTS

Rendered fromdiffHTS.Rmdusingknitr::rmarkdown

Last update: 2026-07-28
Started: 2026-07-28

Help page	Topics
Annotate hits with compound metadata	annotate_hit_info
Stamp a plate-map layout onto measured readings	apply_plate_layout
Subtract the blank background signal from a plate	baseline_subtract
Build a compound-by-sample AUC matrix	build_auc_matrix
Control coefficient of variation per plate	calc_cv
Area under the dose-response curve	calc_drc_auc
Comprehensive per-plate quality assessment	calc_plate_qc
Pairwise replicate correlation between plates	calc_replicate_correlation
Replicate coefficient of variation per compound	calc_replicate_cv
Robust Z'-factor per plate	calc_robust_z_prime
Signal-to-background ratio per plate	calc_sb_ratio
Signal-to-noise ratio per plate	calc_sn_ratio
SSMD per plate (strictly standardised mean difference)	calc_ssmd
Per-well standard and robust Z-scores	calc_well_zscore
Z-factor per plate (sample-aware)	calc_z_factor
Compute per-plate Z' factors	calc_z_prime
Plate-level quality-control metrics for high-throughput screens	calculate_qc_metrics
Validate control-well labelling	check_control_label
Standardise compound identifiers	clean_compound_id
Sanitise a string for use as a file name	clean_filename
Hierarchically cluster an AUC matrix	cluster_auc_matrix
Area under a four-parameter logistic dose-response curve	compute_auc
Differential (delta) AUC between two screening conditions	compute_delta_auc
Convert concentrations to a log10 scale	convert_conc_log10
Flag outlier wells by the IQR rule	detect_outlier_wells
Export a hit summary table	export_hit_table
Extract the most active compound cluster	extract_cluster_hit
Extract dose-response parameters	extract_drc_params
Drop compounds with poor replicate reproducibility	filter_bad_replicate
Drop low-quality dose-response curves	filter_low_quality_curve
Keep only plates that pass the Z' threshold	filter_valid_plates
Fit four-parameter logistic curves per compound	fit_4pl_curve
Fit a four-parameter logistic dose-response model	coef.dsr_4pl fitted.dsr_4pl fit_dose_response predict.dsr_4pl print.dsr_4pl residuals.dsr_4pl
Flag plates that fail quality-control thresholds	flag_qc_plates
Four-parameter logistic (4PL) dose-response function	four_pl
Generate an HTML screening report	generate_hts_report
Example compound metadata	hts_compound_meta
Example gradient dose-response secondary screen	hts_dose_response
Colourblind-safe qualitative palette for diffHTS	hts_pal
Example single 384-well screening plate (realistic layout)	hts_plate_384
Example single-concentration primary screen (raw signals)	hts_primary_raw
Import gradient dose-response data	import_dose_response
Combine normalised plates into one data set	merge_plate_data
Normalise wells to plate controls	norm_by_control
Standard microplate coordinate map	plate_layout plate_layout_1536 plate_layout_384
AUC clustering heatmap	plot_auc_heatmap
Overlay multiple dose-response curves	plot_batch_drc_overlay
Plot the compound clustering dendrogram	plot_cluster_tree
Scatter plot comparing two conditions or cell lines	plot_condition_scatter
Scatter plot of control readouts across plates	plot_control_scatter
Histogram of replicate CV values	plot_cv_distribution
Heatmap of differential AUC across conditions or cell lines	plot_delta_auc_heatmap
Plot dose-response curves for two conditions	plot_dose_response_curves
Hit-count bar chart	plot_hit_bar_count
Stratified hit-count bar chart	plot_hit_stratify_bar
IC50 versus AUC scatter	plot_ic50_auc_cor
Histogram of compound inhibition on a plate	plot_inhibition_hist
Plate-layout heatmap of well readouts	plot_plate_heatmap
Percent-inhibition plate heatmap	plot_plate_heatmap_inhibition
Raw-signal plate heatmap	plot_plate_heatmap_raw
Visualise any plate quality-control metric	plot_plate_qc
Ranked primary-activity curve	plot_primary_inhibition_rank
Primary versus secondary activity correlation	plot_primary_secondary_cor
Quality-control boxplot of control wells across plates	plot_qc_boxplot
Circular heatmap of control readouts across plates	plot_qc_circular_heatmap
Circular plot of a per-plate QC metric	plot_qc_metric_circular
Trend plot of a QC metric across plates	plot_qc_metric_trend
Replicate scatter plot(s) with regression fit and correlation	plot_replicate_scatter
Distribution plot of sigma-based hits	plot_sigma_hits
Plot a single dose-response curve	plot_single_drc
Rank and stratify hit compounds	rank_hit_compound
Import a plate readout file into a standard HTS object	read_hts_plate
Read a user-defined plate-map layout file	read_plate_layout
Example differential-AUC hit table	screen_delta_auc
Example two-condition dose-response screen	screen_doseresponse
Example 96-well plate layout with well positions	screen_plate_layout
Example per-plate quality-control summary	screen_plate_qc
Select hits by an absolute cut-off across conditions	select_hits_cutoff
Select hits by a sigma (z-score) threshold	select_hits_sigma
Select primary-screen hits	select_primary_hit
Select primary-screen hits by distance from the library distribution	select_sigma_hits
Summarise how each plate in a run is set up	summarize_plate_setup
Summarise primary-screen hits	summarize_primary_hit
Summarise sigma-based hits	summarize_sigma_hits
Modern academic ggplot2 theme for diffHTS figures	theme_hts
Convert a Windows path to a forward-slash path	windows_to_linux_path

Package: diffHTS 0.1.0

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)