Package: CDI
Version: 1.6.0
Date: 2023-06-01
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")),
	person("Jichun", "Xie", email = "jichun.xie@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, Seurat, SeuratObject, 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
git_url: https://git.bioconductor.org/packages/CDI
git_branch: RELEASE_3_21
git_last_commit: 6c5ec2f
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 21:04:26 UTC; biocbuild
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],
  Jichun Xie [ctb]
Maintainer: Jiyuan Fang <jfanglovestats@gmail.com>
Built: R 4.5.0; ; 2025-04-16 03:43:28 UTC; unix
