CDI
This is the development version of CDI; for the stable release version, see CDI.
Clustering Deviation Index (CDI)
DOI: 10.18129/B9.bioc.CDI
Bioconductor version: Development (3.24)
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]
Maintainer: Jiyuan Fang <jfanglovestats at gmail.com>
citation("CDI")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Clustering, RNASeq, Sequencing, SingleCell, Software, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | matrixStats, SeuratObject, Seurat, 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | CDI_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | CDI_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | CDI_1.11.0.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 |