Clustering Deviance Index (CDI)

This repository stores the R package of the paper Clustering Deviation Index (CDI): A robust and accurate internal measure for evaluating scRNA-seq data clustering.

Installation guidance

This package has been accepted by Bioconductor. From Oct 2023, you can download the package from Bioconductor by

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CDI")

You can also download the most up-to-date package from Github by running

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("jichunxie/CDI", build_vignettes = TRUE) 

A tutorial of this package can be found by running the following block of codes in R

library(CDI)
browseVignettes("CDI")

Related paper

Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02825-5