{ "_id": "6ab8d91599f7aa8c6aa377d3", "Package": "diffHTS", "Type": "Package", "Title": "Differential Drug Sensitivity Analysis for Two-Condition\nHigh-Throughput Screens", "Version": "0.1.0", "Authors@R": "person(\"Liang\", \"Tang\", email = \"xphdtangliang@gmail.com\", role = c(\"aut\", \"cre\"))", "Description": "A complete workflow for large-scale, two-condition\nhigh-throughput drug screening (HTS). It compares drug\nsensitivity between any two experimental conditions - for\nexample irradiated versus non-irradiated cells, cancer versus\nnormal cell lines, or treated versus untreated samples - across\nmany plates and experiments. The package covers the full\npipeline: control-based normalisation, plate-level\nquality-control metrics (Z-factor, Z-prime,\nsignal-to-background, signal-to-noise and strictly standardised\nmean difference), replicate-consistency checks, four-parameter\nlogistic dose-response fitting with area under the curve (AUC)\nestimation, differential (delta) AUC scoring with within-plate\nstandardisation, cut-off and sigma-based hit selection, and\npublication-ready heatmap, scatter and quality-control\nvisualisations.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-27 08:46:31 UTC", "User": "root" }, "Author": "Liang Tang [aut, cre]", "Maintainer": "Liang Tang ", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://kongjianyang.r-universe.dev", "Date/Publication": "2026-07-28 16:10:08 UTC", "RemoteUrl": "https://github.com/cran/diffHTS", "RemoteRef": "HEAD", "RemoteSha": "67aacbc0505a58ec8a1a04573ff36e297e95b633", "_user": "kongjianyang", "_type": "src", "_file": "diffHTS_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/5a14d82110ba82ad2e9a456bc86fe876e920c250f01fcf777a49037d030443c3", "_filesize": 3696454, "_sha256": "5a14d82110ba82ad2e9a456bc86fe876e920c250f01fcf777a49037d030443c3", "_expires": "2027-01-05T08:51:30.000Z", "_created": "2026-09-27T08:46:31.000Z", "_published": "2026-09-27T08:51:33.121Z", "_jobs": [ { "job": 108586276546, "time": 181, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10928201083" }, { "job": 108586276646, "time": 169, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10927597252" }, { "job": 108586276629, "time": 178, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10927733059" }, { "job": 108586276633, "time": 158, "config": "macos-release-arm64", "r": "4.6.1", "check": 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1785255008 }, "_maintainer": { "name": "Liang Tang", "email": "xphdtangliang@gmail.com", "login": "kongjianyang", "description": "Bioinformatician in healthcare\n", "uuid": 13445428 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "tidyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "ggprism", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-31", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-07-28" } ], "_stars": 0, "_contributors": [ { "user": "kongjianyang", "count": 1, "uuid": 13445428 } ], "_userbio": { "uuid": 13445428, "type": "user", "name": "Tang", "followers": 0, "description": "Bioinformatician in healthcare" }, "_downloads": { "count": 344, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/diffHTS" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/diffHTS.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_realowner": "kongjianyang", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-07-28" } ], "_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" ], "_datasets": [ { "name": "hts_compound_meta", "title": "Example compound metadata", "object": "hts_compound_meta", "class": [ "data.frame" ], "fields": [ "compound_id", "compound_name", "target", "moa", "library_source" ], "rows": 48, "table": true, "tojson": true }, { "name": "hts_dose_response", "title": "Example gradient dose-response secondary screen", "object": "hts_dose_response", "class": [ "data.frame" ], "fields": [ "compound_id", "cell_line", "concentration", "replicate", "viability" ], "rows": 480, "table": true, "tojson": true }, { "name": "hts_plate_384", "title": "Example single 384-well screening plate (realistic layout)", "object": "hts_plate_384", "class": [ "data.frame" ], "fields": [ "plate_id", "well", "row", "col", "well_type", "compound_id", "concentration", "signal" ], "rows": 384, "table": true, "tojson": true }, { "name": "hts_primary_raw", "title": "Example single-concentration primary screen (raw signals)", "object": "hts_primary_raw", "class": [ "data.frame" ], "fields": [ "plate_id", "well", "row", "col", "well_type", "compound_id", "concentration", "signal" ], "rows": 288, "table": true, "tojson": true }, { "name": "screen_delta_auc", "title": "Example differential-AUC hit table", "object": "screen_delta_auc", "class": [ "data.frame" ], "fields": [ "drug_name", "A549", "H1299", "H1975", "H2030", "MRC5" ], "rows": 30, "table": true, "tojson": true }, { "name": "screen_doseresponse", "title": "Example two-condition dose-response screen", "object": "screen_doseresponse", "class": [ "data.frame" ], "fields": [ "plateID", "drug_name", "experiment_type", "condition", "concentration", "normalized_cell_count" ], "rows": 152, "table": true, "tojson": true }, { "name": "screen_plate_layout", "title": "Example 96-well plate layout with well positions", "object": "screen_plate_layout", "class": [ "data.frame" ], "fields": [ "plateID", "condition", "well", "plate_rows", "plate_columns", "drug_name", "experiment_type", "concentration", "normalized_cell_count" ], "rows": 192, "table": true, "tojson": true }, { "name": "screen_plate_qc", "title": "Example per-plate quality-control summary", "object": "screen_plate_qc", "class": [ "data.frame" ], "fields": [ "plateID", "experimentID", "cell_line", "plateNumber", "z_factor", "z_prime", "sb_value", "sn_value", "ssmd_value", "cv_negative_ctrl", "neg_ctrl_1", "neg_ctrl_2", "neg_ctrl_3", "neg_ctrl_4", "neg_ctrl_5", "neg_ctrl_6", "pos_ctrl_1", "pos_ctrl_2", "pos_ctrl_3", "pos_ctrl_4", "pos_ctrl_5", "pos_ctrl_6" ], "rows": 60, "table": true, "tojson": true } ], "_help": [ { "page": "annotate_hit_info", "title": "Annotate hits with compound metadata", "topics": [ "annotate_hit_info" ] }, { "page": "apply_plate_layout", "title": "Stamp a plate-map layout onto measured readings", "topics": [ "apply_plate_layout" ] }, { "page": "baseline_subtract", "title": "Subtract the blank background signal from a plate", "topics": [ "baseline_subtract" ] }, { "page": "build_auc_matrix", "title": "Build a compound-by-sample AUC matrix", "topics": [ "build_auc_matrix" ] }, { "page": "calc_cv", "title": "Control coefficient of variation per plate", "topics": [ "calc_cv" ] }, { "page": "calc_drc_auc", "title": "Area under the dose-response curve", "topics": [ "calc_drc_auc" ] }, { "page": "calc_plate_qc", "title": "Comprehensive per-plate quality assessment", "topics": [ "calc_plate_qc" ] }, { "page": "calc_replicate_correlation", "title": "Pairwise replicate correlation between plates", "topics": [ "calc_replicate_correlation" ] }, { "page": "calc_replicate_cv", "title": "Replicate coefficient of variation per compound", "topics": [ "calc_replicate_cv" ] }, { "page": "calc_robust_z_prime", "title": "Robust Z'-factor per plate", "topics": [ "calc_robust_z_prime" ] }, { "page": "calc_sb_ratio", "title": "Signal-to-background ratio per plate", "topics": [ "calc_sb_ratio" ] }, { "page": "calc_sn_ratio", "title": "Signal-to-noise ratio per plate", "topics": [ "calc_sn_ratio" ] }, { "page": "calc_ssmd", "title": "SSMD per plate (strictly standardised mean difference)", "topics": [ "calc_ssmd" ] }, { "page": "calc_well_zscore", "title": "Per-well standard and robust Z-scores", "topics": [ "calc_well_zscore" ] }, { "page": "calc_z_factor", "title": "Z-factor per plate (sample-aware)", "topics": [ "calc_z_factor" ] }, { "page": "calc_z_prime", "title": "Compute per-plate Z' factors", "topics": [ "calc_z_prime" ] }, { "page": "calculate_qc_metrics", "title": "Plate-level quality-control metrics for high-throughput screens", "topics": [ "calculate_qc_metrics" ] }, { "page": "check_control_label", "title": "Validate control-well labelling", "topics": [ "check_control_label" ] }, { "page": "clean_compound_id", "title": "Standardise compound identifiers", "topics": [ "clean_compound_id" ] }, { "page": "clean_filename", "title": "Sanitise a string for use as a file name", "topics": [ "clean_filename" ] }, { "page": "cluster_auc_matrix", "title": "Hierarchically cluster an AUC matrix", "topics": [ "cluster_auc_matrix" ] }, { "page": "compute_auc", "title": "Area under a four-parameter logistic dose-response curve", "topics": [ "compute_auc" ] }, { "page": "compute_delta_auc", "title": "Differential (delta) AUC between two screening conditions", "topics": [ "compute_delta_auc" ] }, { "page": "convert_conc_log10", "title": "Convert concentrations to a log10 scale", "topics": [ "convert_conc_log10" ] }, { "page": "detect_outlier_wells", "title": "Flag outlier wells by the IQR rule", "topics": [ "detect_outlier_wells" ] }, { "page": "export_hit_table", "title": "Export a hit summary table", "topics": [ "export_hit_table" ] }, { "page": "extract_cluster_hit", "title": "Extract the most active compound cluster", "topics": [ "extract_cluster_hit" ] }, { "page": "extract_drc_params", "title": "Extract dose-response parameters", "topics": [ "extract_drc_params" ] }, { "page": "filter_bad_replicate", "title": "Drop compounds with poor replicate reproducibility", "topics": [ "filter_bad_replicate" ] }, { "page": "filter_low_quality_curve", "title": "Drop low-quality dose-response curves", "topics": [ "filter_low_quality_curve" ] }, { "page": "filter_valid_plates", "title": "Keep only plates that pass the Z' threshold", "topics": [ "filter_valid_plates" ] }, { "page": "fit_4pl_curve", "title": "Fit four-parameter logistic curves per compound", "topics": [ "fit_4pl_curve" ] }, { "page": "fit_dose_response", "title": "Fit a four-parameter logistic dose-response model", "topics": [ "coef.dsr_4pl", "fitted.dsr_4pl", "fit_dose_response", "predict.dsr_4pl", "print.dsr_4pl", "residuals.dsr_4pl" ] }, { "page": "flag_qc_plates", "title": "Flag plates that fail quality-control thresholds", "topics": [ "flag_qc_plates" ] }, { "page": "four_pl", "title": "Four-parameter logistic (4PL) dose-response function", "topics": [ "four_pl" ] }, { "page": "generate_hts_report", "title": "Generate an HTML screening report", "topics": [ "generate_hts_report" ] }, { "page": "hts_compound_meta", "title": "Example compound metadata", "topics": [ "hts_compound_meta" ] }, { "page": "hts_dose_response", "title": "Example gradient dose-response secondary screen", "topics": [ "hts_dose_response" ] }, { "page": "hts_pal", "title": "Colourblind-safe qualitative palette for diffHTS", "topics": [ "hts_pal" ] }, { "page": "hts_plate_384", "title": "Example single 384-well screening plate (realistic layout)", "topics": [ "hts_plate_384" ] }, { "page": "hts_primary_raw", "title": "Example single-concentration primary screen (raw signals)", "topics": [ "hts_primary_raw" ] }, { "page": "import_dose_response", "title": "Import gradient dose-response data", "topics": [ "import_dose_response" ] }, { "page": "merge_plate_data", "title": "Combine normalised plates into one data set", "topics": [ "merge_plate_data" ] }, { "page": "norm_by_control", "title": "Normalise wells to plate controls", "topics": [ "norm_by_control" ] }, { "page": "plate_layout", "title": "Standard microplate coordinate map", "topics": [ "plate_layout", "plate_layout_1536", "plate_layout_384" ] }, { "page": "plot_auc_heatmap", "title": "AUC clustering heatmap", "topics": [ "plot_auc_heatmap" ] }, { "page": "plot_batch_drc_overlay", "title": "Overlay multiple dose-response curves", "topics": [ "plot_batch_drc_overlay" ] }, { "page": "plot_cluster_tree", "title": "Plot the compound clustering dendrogram", "topics": [ "plot_cluster_tree" ] }, { "page": "plot_condition_scatter", "title": "Scatter plot comparing two conditions or cell lines", "topics": [ "plot_condition_scatter" ] }, { "page": "plot_control_scatter", "title": "Scatter plot of control readouts across plates", "topics": [ "plot_control_scatter" ] }, { "page": "plot_cv_distribution", "title": "Histogram of replicate CV values", "topics": [ "plot_cv_distribution" ] }, { "page": "plot_delta_auc_heatmap", "title": "Heatmap of differential AUC across conditions or cell lines", "topics": [ "plot_delta_auc_heatmap" ] }, { "page": "plot_dose_response_curves", "title": "Plot dose-response curves for two conditions", "topics": [ "plot_dose_response_curves" ] }, { "page": "plot_hit_bar_count", "title": "Hit-count bar chart", "topics": [ "plot_hit_bar_count" ] }, { "page": "plot_hit_stratify_bar", "title": "Stratified hit-count bar chart", "topics": [ "plot_hit_stratify_bar" ] }, { "page": "plot_ic50_auc_cor", "title": "IC50 versus AUC scatter", "topics": [ "plot_ic50_auc_cor" ] }, { "page": "plot_inhibition_hist", "title": "Histogram of compound inhibition on a plate", "topics": [ "plot_inhibition_hist" ] }, { "page": "plot_plate_heatmap", "title": "Plate-layout heatmap of well readouts", "topics": [ "plot_plate_heatmap" ] }, { "page": "plot_plate_heatmap_inhibition", "title": "Percent-inhibition plate heatmap", "topics": [ "plot_plate_heatmap_inhibition" ] }, { "page": "plot_plate_heatmap_raw", "title": "Raw-signal plate heatmap", "topics": [ "plot_plate_heatmap_raw" ] }, { "page": "plot_plate_qc", "title": "Visualise any plate quality-control metric", "topics": [ "plot_plate_qc" ] }, { "page": "plot_primary_inhibition_rank", "title": "Ranked primary-activity curve", "topics": [ "plot_primary_inhibition_rank" ] }, { "page": "plot_primary_secondary_cor", "title": "Primary versus secondary activity correlation", "topics": [ "plot_primary_secondary_cor" ] }, { "page": "plot_qc_boxplot", "title": "Quality-control boxplot of control wells across plates", "topics": [ "plot_qc_boxplot" ] }, { "page": "plot_qc_circular_heatmap", "title": "Circular heatmap of control readouts across plates", "topics": [ "plot_qc_circular_heatmap" ] }, { "page": "plot_qc_metric_circular", "title": "Circular plot of a per-plate QC metric", "topics": [ "plot_qc_metric_circular" ] }, { "page": "plot_qc_metric_trend", "title": "Trend plot of a QC metric across plates", "topics": [ "plot_qc_metric_trend" ] }, { "page": "plot_replicate_scatter", "title": "Replicate scatter plot(s) with regression fit and correlation", "topics": [ "plot_replicate_scatter" ] }, { "page": "plot_sigma_hits", "title": "Distribution plot of sigma-based hits", "topics": [ "plot_sigma_hits" ] }, { "page": "plot_single_drc", "title": "Plot a single dose-response curve", "topics": [ "plot_single_drc" ] }, { "page": "rank_hit_compound", "title": "Rank and stratify hit compounds", "topics": [ "rank_hit_compound" ] }, { "page": "read_hts_plate", "title": "Import a plate readout file into a standard HTS object", "topics": [ "read_hts_plate" ] }, { "page": "read_plate_layout", "title": "Read a user-defined plate-map layout file", "topics": [ "read_plate_layout" ] }, { "page": "screen_delta_auc", "title": "Example differential-AUC hit table", "topics": [ "screen_delta_auc" ] }, { "page": "screen_doseresponse", "title": "Example two-condition dose-response screen", "topics": [ "screen_doseresponse" ] }, { "page": "screen_plate_layout", "title": "Example 96-well plate layout with well positions", "topics": [ "screen_plate_layout" ] }, { "page": "screen_plate_qc", "title": "Example per-plate quality-control summary", "topics": [ "screen_plate_qc" ] }, { "page": "select_hits_cutoff", "title": "Select hits by an absolute cut-off across conditions", "topics": [ "select_hits_cutoff" ] }, { "page": "select_hits_sigma", "title": "Select hits by a sigma (z-score) threshold", "topics": [ "select_hits_sigma" ] }, { "page": "select_primary_hit", "title": "Select primary-screen hits", "topics": [ "select_primary_hit" ] }, { "page": "select_sigma_hits", "title": "Select primary-screen hits by distance from the library distribution", "topics": [ "select_sigma_hits" ] }, { "page": "summarize_plate_setup", "title": "Summarise how each plate in a run is set up", "topics": [ "summarize_plate_setup" ] }, { "page": "summarize_primary_hit", "title": "Summarise primary-screen hits", "topics": [ "summarize_primary_hit" ] }, { "page": "summarize_sigma_hits", "title": "Summarise sigma-based hits", "topics": [ "summarize_sigma_hits" ] }, { "page": "theme_hts", "title": "Modern academic ggplot2 theme for diffHTS figures", "topics": [ "theme_hts" ] }, { "page": "windows_to_linux_path", "title": "Convert a Windows path to a forward-slash path", "topics": [ "windows_to_linux_path" ] } ], "_readme": "https://github.com/cran/diffHTS/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", 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