Canek: Batch Correction of Single Cell Transcriptome Data
Non-linear/linear hybrid method for batch-effect correction that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
| Version: | 0.2.5 |
| Depends: | R (≥ 3.5.0) |
| Imports: | FNN, irlba, numbers, fpc, bluster, igraph, matrixStats, utils |
| Suggests: | testthat (≥ 2.1.0), Seurat, SingleCellExperiment, SummarizedExperiment, scater, batchelor, scran, knitr, rmarkdown, patchwork, ggplot2 |
| Published: | 2023-12-08 |
| DOI: | 10.32614/CRAN.package.Canek |
| Author: | Martin Loza  [aut,
cre],
Diego Diez [aut] |
| Maintainer: | Martin Loza <martin.loza.lopez at gmail.com> |
| BugReports: | https://github.com/MartinLoza/Canek/issues |
| License: | MIT + file LICENSE |
| URL: | https://martinloza.github.io/Canek/ |
| NeedsCompilation: | no |
| Citation: | Canek citation info |
| Materials: | README NEWS |
| CRAN checks: | Canek results |
Documentation:
| Reference manual: | Canek.pdf |
| Vignettes: |
Run Canek on a toy example (source, R code) |
Downloads:
| Package source: | Canek_0.2.5.tar.gz |
| Windows binaries: | r-devel: Canek_0.2.5.zip, r-release: Canek_0.2.5.zip, r-oldrel: Canek_0.2.5.zip |
| macOS binaries: | r-devel (arm64): Canek_0.2.5.tgz, r-release (arm64): Canek_0.2.5.tgz, r-oldrel (arm64): Canek_0.2.5.tgz, r-devel (x86_64): Canek_0.2.5.tgz, r-release (x86_64): Canek_0.2.5.tgz, r-oldrel (x86_64): Canek_0.2.5.tgz |
| Old sources: | Canek archive |
Linking:
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