An R package for analyzing multi-dimensional high-throughput screening data, particularly two-dimensional RNAi screens and single-cell RNA sequencing data.
# Install from CRAN
install.packages("ZetaSuite")
# Or install from GitHub
::install_github("username/ZetaSuite")
devtools
# Load the package
library(ZetaSuite)
# Load example data
data(countMat)
data(negGene)
data(posGene)
data(nonExpGene)
# Quality Control
<- QC(countMat, negGene, posGene)
qc_results
# Z-score normalization
<- Zscore(countMat, negGene)
zscore_matrix
# Event coverage analysis
<- EventCoverage(zscore_matrix, negGene, posGene)
ec_results
# Zeta score calculation
<- Zeta(zscore_matrix, ec_results[[1]]$ZseqList)
zeta_scores
# FDR cutoff analysis
<- FDRcutoff(zeta_scores, negGene, posGene, nonExpGene) fdr_results
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
For detailed documentation and examples, see the package vignette:
vignette("ZetaSuite")
If you encounter any bugs or have feature requests, please report them on our GitHub issues page:
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
This package is licensed under the MIT License - see the LICENSE file for details.