CDI
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see CDI.
Clustering Deviation Index (CDI)
DOI: 10.18129/B9.bioc.CDI
Bioconductor version: 3.21
Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.
Author: Jiyuan Fang [cre, aut] ORCID iD ORCID: 0000-0002-5004-4138 , Jichun Xie [ctb], Cliburn Chan [ctb], Kouros Owzar [ctb], Liuyang Wang [ctb], Diyuan Qin [ctb], Qi-Jing Li [ctb], Jichun Xie [ctb]
Maintainer: Jiyuan Fang <jfanglovestats at gmail.com>
citation("CDI")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CDI")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CDI")
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