Package: CDI
Version: 1.11.0
Date: 2026-03-15
Title: Clustering Deviation Index (CDI)
Description: 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.
Authors@R: c(person("Jiyuan", "Fang", email = "jfanglovestats@gmail.com", role = c("cre", "aut"), comment=c(ORCID="0000-0002-5004-4138")), 
	person("Jichun", "Xie", email = "jichun.xie@duke.edu", role = c("ctb")),
	person("Cliburn", "Chan", email = "cliburn.chan@duke.edu", role = c("ctb")),
	person("Kouros", "Owzar", email = "kouros.owzar@duke.edu", role = c("ctb")),
	person("Liuyang", "Wang", email = "liuyang.wang@duke.edu", role = c("ctb")),
	person("Diyuan", "Qin", email = "diyuan.qin@duke.edu", role = c("ctb")),
	person("Qi-Jing", "Li", email = "qi-jing.li@duke.edu", role = c("ctb")))
biocViews: SingleCell, Software, Clustering, Visualization, Sequencing,
        RNASeq, CellBasedAssays
URL: https://github.com/jichunxie/CDI
BugReports: https://github.com/jichunxie/CDI/issues
Imports: matrixStats, SeuratObject, Seurat, stats, BiocParallel,
        ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment,
        SummarizedExperiment, methods
RoxygenNote: 7.2.3
Depends: R(>= 3.6)
Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
VignetteBuilder: knitr
License: GPL-3 + file LICENSE
Encoding: UTF-8
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:01:09 UTC
RemoteUrl: https://github.com/bioc/CDI
RemoteRef: HEAD
RemoteSha: 191ae443191765e67e31d38ed1a0da1df314157c
NeedsCompilation: no
Packaged: 2026-07-18 04:53:09 UTC; root
Author: Jiyuan Fang [cre, aut] (ORCID: <https://orcid.org/0000-0002-5004-4138>),
  Jichun Xie [ctb],
  Cliburn Chan [ctb],
  Kouros Owzar [ctb],
  Liuyang Wang [ctb],
  Diyuan Qin [ctb],
  Qi-Jing Li [ctb]
Maintainer: Jiyuan Fang <jfanglovestats@gmail.com>