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ZetaSuite

An R package for analyzing multi-dimensional high-throughput screening data, particularly two-dimensional RNAi screens and single-cell RNA sequencing data.

Installation

# Install from CRAN
install.packages("ZetaSuite")

# Or install from GitHub
devtools::install_github("username/ZetaSuite")

# Load the package
library(ZetaSuite)

Quick Start

# Load example data
data(countMat)
data(negGene)
data(posGene)
data(nonExpGene)

# Quality Control
qc_results <- QC(countMat, negGene, posGene)

# Z-score normalization
zscore_matrix <- Zscore(countMat, negGene)

# Event coverage analysis
ec_results <- EventCoverage(zscore_matrix, negGene, posGene)

# Zeta score calculation
zeta_scores <- Zeta(zscore_matrix, ec_results[[1]]$ZseqList)

# FDR cutoff analysis
fdr_results <- FDRcutoff(zeta_scores, negGene, posGene, nonExpGene)

Interactive Shiny Application

Launch the interactive web interface for ZetaSuite:

# Launch the Shiny app
ZetaSuiteApp()

# Launch without opening browser automatically
ZetaSuiteApp(launch.browser = FALSE)

# Launch on a specific port
ZetaSuiteApp(port = 3838)

The Shiny app provides: - Interactive data upload and visualization - Step-by-step analysis workflow - Real-time results and plots - Data export capabilities - Built-in example dataset

Features

• Quality Control Analysis: Comprehensive evaluation of experimental design and data quality
• Z-score Normalization: Standardization using negative controls as reference
• Event Coverage Analysis: Quantification of regulatory effects across thresholds
• Zeta Score Calculation: Area-under-curve based scoring for regulatory effects
• SVM-based Background Correction: Machine learning approach to filter noise
• Screen Strength Analysis: Optimal threshold selection for hit identification
• Single Cell Quality Control: Cell quality assessment for scRNA-seq data

Documentation

For detailed documentation and examples, see the package vignette:

vignette("ZetaSuite")

Bug Reports

If you encounter any bugs or have feature requests, please report them on our GitHub issues page:

Report a Bug

Citation

If you use ZetaSuite in your research, please cite:

Hao, Y., Zhang, S., Shao, C. et al. ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics. Genome Biol 23, 162 (2022). https://doi.org/10.1186/s13059-022-02729-4

License

This package is licensed under the MIT License - see the LICENSE file for details.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.