Package: Canek 0.2.5

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>.

Authors:Martin Loza [aut, cre], Diego Diez [aut]

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Canek.pdf |Canek.html✨
Canek/json (API)
NEWS

# Install 'Canek' in R:
install.packages('Canek', repos = c('https://martinloza.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/martinloza/canek/issues

Pkgdown site:https://martinloza.github.io

Datasets:
  • SimBatches - Dataset with simulated single cell RNA-seq from 2 batches.

On CRAN:

Conda:

batch-effectsbioinformaticssingle-cell-rna-seqtranscriptomics

5.06 score 5 stars 23 scripts 260 downloads 3 exports 43 dependencies

Last updated 1 years agofrom:26075598fe. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 30 2025
R-4.5-winOKMar 30 2025
R-4.5-macOKMar 30 2025
R-4.5-linuxOKMar 30 2025
R-4.4-winOKMar 30 2025
R-4.4-macOKMar 30 2025
R-4.4-linuxOKMar 30 2025
R-4.3-winOKMar 30 2025
R-4.3-macOKMar 30 2025

Exports:CorrectBatchCorrectBatchesRunCanek

Dependencies:assortheadBHBiocGenericsBiocNeighborsBiocParallelblusterclasscliclustercodetoolscpp11DEoptimRdiptestflexmixFNNformatRfpcfutile.loggerfutile.optionsgenericsglueigraphirlbakernlablambda.rlatticelifecyclemagrittrMASSMatrixmatrixStatsmclustmodeltoolsnnetnumberspkgconfigprabclusRcpprlangrobustbaseS4Vectorssnowvctrs

Run Canek on a toy example

Rendered fromtoy_example.Rmdusingknitr::rmarkdownon Mar 30 2025.

Last update: 2022-03-22
Started: 2021-06-17

Readme and manuals

Help Manual

Help pageTopics
CheckZeroCVCheckZeroCV
CorrectBatchCorrectBatch
CorrectBatchesCorrectBatches
Correction vector estimationEkfBE
Title FuzzyFuzzy
MeanBEMeanBE
Correction vector estimationMedianBE
Title PairsFilteringPairsFiltering
RunCanekRunCanek RunCanek.list RunCanek.Seurat RunCanek.SingleCellExperiment
Dataset with simulated single cell RNA-seq from 2 batches.SimBatches