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]

Canek_0.2.5.tar.gz
Canek_0.2.5.zip(r-4.7)Canek_0.2.5.zip(r-4.6)Canek_0.2.5.zip(r-4.5)
Canek_0.2.5.tgz(r-4.6-any)Canek_0.2.5.tgz(r-4.5-any)
Canek_0.2.5.tar.gz(r-4.7-any)Canek_0.2.5.tar.gz(r-4.6-any)
Canek_0.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Canek/json (API)

# 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/docs site:https://martinloza.github.io

Datasets:

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

On CRAN:

batch-effects bioinformatics single-cell-rna-seq transcriptomics

5.24 score 7 stars 25 scripts 375 downloads 3 exports 51 dependencies

Last updated from:26075598fe. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	253
source / vignettes	OK	276
linux-release-x86_64	OK	247
macos-release-arm64	OK	252
macos-oldrel-arm64	OK	231
windows-devel	OK	190
windows-release	OK	203
windows-oldrel	OK	209
wasm-release	OK	197

Exports:CorrectBatch CorrectBatches RunCanek

Dependencies:abind assorthead beachmat BH BiocGenerics BiocNeighbors BiocParallel bluster class cli cluster codetools cpp11 DelayedArray DEoptimR diptest flexmix FNN formatR fpc futile.logger futile.options generics glue igraph IRanges irlba kernlab lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust modeltools nnet numbers pkgconfig prabclus Rcpp rlang robustbase S4Arrays S4Vectors snow SparseArray vctrs XVector

Run Canek on a toy example

Load the data | PCA before correction | Run Canek | PCA after correction | Session info

Rendered fromtoy_example.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CheckZeroCV	CheckZeroCV
CorrectBatch	CorrectBatch
CorrectBatches	CorrectBatches
Correction vector estimation	EkfBE
Title Fuzzy	Fuzzy
MeanBE	MeanBE
Correction vector estimation	MedianBE
Title PairsFiltering	PairsFiltering
RunCanek	RunCanek RunCanek.list RunCanek.Seurat RunCanek.SingleCellExperiment
Dataset with simulated single cell RNA-seq from 2 batches.	SimBatches