CGExplorer: Chemo-Genomic Screening Data Preprocessor & Visualizer

CGExplorer is an R package and Shiny application designed for lab researchers to quickly preprocess, perform quality control, analyze, and visualize high-throughput Chemo-Genomic Screening datasets (such as plate reader outputs for bacterial mutant libraries under chemical/drug treatments).

The package provides S4 data structures (Plate, Batch, PlateRegistry), automated data preprocessing pipelines, chemo-genomic interaction scoring, interactive plotly visualizations, and a full-featured Shiny GUI.

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Key Features

• S4 Data Architecture:
  • Plate: Manages raw Tecan reader data (growth, staining), 384-well layout metadata, computed kinetic metrics, and QC flags.
  • Batch: Groups plates across experimental replicates and stores multi-replicate interaction scoring results.
  • PlateRegistry: Manages persistent local state across user sessions and package upgrades.
• Automated Data Assembly: Pairs raw Tecan plate reader output files (.txt) with 384-well layout templates (.xlsx/.tsv).
• Growth & Biofilm Metrics: Calculates kinetic parameters (AUC, Max OD, Max Rate, Duration, Endpoint OD) and stained biofilm metrics (Mean OD, Relative Biofilm index).
• Staining Detection: Automated jump detection algorithm (detect_staining_jump) to identify staining timepoints.
• Quality Control Pipeline: Identifies contaminated blank wells, evaluates wild-type (WT) control growth, and flags anomalous wells.
• Chemo-Genomic Interaction Scoring: Scores chemical-gene interactions (linear & $\log_2$ interaction scores, $z$-scores, FDR adjustment) with single-replicate or batch-merged strategies (mean, min, max).
• Interactive Visualizations: Powered by plotly for interactive growth curves, rank-ordered hit plots, plate layout heatmaps, and mutant-level replicate overlays.
• Data Export: Direct UI export of hit tables, QC logs, and well-level metrics to CSV or Excel (.xlsx) files.

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Installation

# Install pak if not already installed
if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}

# Install CGExplorer package
# pak::pak("zqzneptune/CGExplorer")
install.packages("CGExplorer", repos = c('https://zqzneptune.r-universe.dev', 'https://cloud.r-project.org'))

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Launching the Interactive Shiny App

library(CGExplorer)

# Launch the Shiny application
run_cgexplorer_app()

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License

Distributed under the MIT License. Copyright (c) 2026 QINGZHOU ZHANG.