CyEMD: A differential analysis method developed for CyTOF data

The CyEMD R package provides a differential analysis method that is based on calculating the Earth Mover´s Distance between expression distributions. It can handle strong zero-inflation without being too sensitive.

Installation

Currently the package is only available on GitHub. For installation use one of the following possibilities:

1. The package can be directly installed from GitHub running

   remotes::install_github("https://github.com/biomedbigdata/CyEMD_package.git")

2. The package can be installed after cloning the repository running

   devtools::install("~/path/to/package")

Dependencies

R >= 4.2

Packages available on CRAN:

• data.table
• Rcpp
• RcppAlgos
• stats
• graphics

Packages available on Bioconductor:

• SummarizedExperiment
• CATALYST

Cite

Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List, A systematic comparison of novel and existing differential analysis methods for CyTOF data, Briefings in Bioinformatics, Volume 23, Issue 1, January 2022, bbab471, https://doi.org/10.1093/bib/bbab471