A pipeline to analyze high-throughput fluorescence cytometry data, flow cytometry and mass cytometry, in which there naturally are hundreds of samples to analyze in parallel like in drug-dose response analysis. The pipeline integrates the following steps:
- Compensating samples (fcs files)
- Correcting signal drift (batch effect) in samples
- Generating similarity matrix of samples
- Generating similarity heatmap of samples
- Clustering of samples
- Interpretations of results
To install the pipleline, simply download the zip file or clone the repository. The pipleine needs the following conventional R pakackges to run:
- compaRe
- parallel
- flowCore
- pheatmap
- igraph
- ggplot2
- gridExtra