CDI

This is the development version of CDI; for the stable release version, see CDI.

Clustering Deviation Index (CDI)

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("CDI")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Clustering Deviation Index (CDI) Tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, Clustering, RNASeq, Sequencing, SingleCell, Software, Visualization
Version	1.1.1
In Bioconductor since	BioC 3.18 (R-4.3) (0.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.6)
Imports	matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods
System Requirements
URL	https://github.com/jichunxie/CDI
Bug Reports	https://github.com/jichunxie/CDI/issues

Suggests	knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CDI_1.1.1.tar.gz
Windows Binary	CDI_1.1.1.zip
macOS Binary (x86_64)	CDI_1.1.1.tgz
macOS Binary (arm64)	CDI_1.1.1.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