CIDER: Meta-Clustering for scRNA-Seq Integration and Evaluation

A workflow of (a) meta-clustering based on inter-group similarity measures and (b) a ground-truth-free test metric to assess the biological correctness of integration in real datasets. See Hu Z, Ahmed A, Yau C (2021) <doi:10.1101/2021.03.29.437525> for more details.

Version:	0.99.4
Depends:	R (≥ 3.5.0)
Imports:	limma (≥ 3.42.0), edgeR (≥ 3.28.0), stats (≥ 3.6.2), foreach (≥ 1.4.7), Seurat (≥ 3.1.0), utils (≥ 3.6.2), pheatmap (≥ 1.0.0), dbscan (≥ 1.1-5), kernlab (≥ 0.9-29), doParallel, igraph, parallel, graphics, ggplot2, viridis
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), statmod (≥ 1.2.2), cowplot
Published:	2025-02-07
DOI:	10.32614/CRAN.package.CIDER
Author:	Zhiyuan Hu [aut, cre], Christopher Yau [aut], Ahmed Ahmed [aut]
Maintainer:	Zhiyuan Hu <zhiyuan.cheryl.hu at gmail.com>
BugReports:	https://github.com/zhiyuan-hu-lab/CIDER/issues
License:	MIT + file LICENSE
URL:	https://github.com/zhiyuan-hu-lab/CIDER, https://zhiyuan-hu-lab.github.io/CIDER/
NeedsCompilation:	no
Materials:	README NEWS
CRAN checks:	CIDER results

Documentation:

Reference manual:	CIDER.pdf
Vignettes:	Getting Start with Assisted CIDER (asCIDER) (source, R code) Evaluating scRNA-seq Integration Quality with CIDER (source, R code)

Downloads:

Package source:	CIDER_0.99.4.tar.gz
Windows binaries:	r-devel: CIDER_0.99.4.zip, r-release: CIDER_0.99.4.zip, r-oldrel: CIDER_0.99.4.zip
macOS binaries:	r-release (arm64): CIDER_0.99.4.tgz, r-oldrel (arm64): not available, r-release (x86_64): CIDER_0.99.4.tgz, r-oldrel (x86_64): not available
Old sources:	CIDER archive

Linking:

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