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: 0.2.1
Depends: R (≥ 2.10)
Imports: FNN, irlba, numbers, fpc, bluster, igraph, matrixStats
Suggests: testthat (≥ 2.1.0), Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown
Published: 2022-05-10
Author: Martin Loza ORCID iD [aut, cre], Diego Diez ORCID iD [aut]
Maintainer: Martin Loza <martin.loza.lopez at gmail.com>
License: MIT + file LICENSE
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

Downloads:

Package source: Canek_0.2.1.tar.gz
Windows binaries: r-devel: Canek_0.2.1.zip, r-release: Canek_0.2.1.zip, r-oldrel: Canek_0.2.1.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): Canek_0.2.1.tgz, r-release (x86_64): Canek_0.2.1.tgz, r-oldrel (x86_64): Canek_0.2.1.tgz
Old sources: Canek archive

Linking:

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