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-devel (arm64): CIDER_0.99.4.tgz, r-release (arm64): CIDER_0.99.4.tgz, r-oldrel (arm64): CIDER_0.99.4.tgz, r-devel (x86_64): CIDER_0.99.4.tgz, r-release (x86_64): CIDER_0.99.4.tgz, r-oldrel (x86_64): CIDER_0.99.4.tgz |
| Old sources: | CIDER archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=CIDER to link to this page.