CDI

DOI: 10.18129/B9.bioc.CDI  

Clustering Deviation Index (CDI)

Bioconductor version: Release (3.18)

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] , 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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	CellBasedAssays, Clustering, RNASeq, Sequencing, SingleCell, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3 + file LICENSE
Depends	R (>= 3.6)
Imports	matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods
LinkingTo
Suggests	knitr, rmarkdown, RUnit, BiocGenerics, magick
SystemRequirements
Enhances
URL	https://github.com/jichunxie/CDI
BugReports	https://github.com/jichunxie/CDI/issues
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary	CDI_1.0.0.zip
macOS Binary (x86_64)	CDI_1.0.0.tgz
macOS Binary (arm64)	CDI_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CDI
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CDI
Bioc Package Browser	https://code.bioconductor.org/browse/CDI/
Package Short Url	https://bioconductor.org/packages/CDI/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive