CDI
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CDI.
Clustering Deviation Index (CDI)
Bioconductor version: 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("CDI")):
Installation
To install this package, start R (version "4.4") 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")| Clustering Deviation Index (CDI) Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Clustering, RNASeq, Sequencing, SingleCell, Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 |
See More
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | CDI_1.2.0.zip |
| macOS Binary (x86_64) | CDI_1.2.0.tgz |
| macOS Binary (arm64) | CDI_1.2.0.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 |