Canek

Citation

If you use Canek in your research please cite our work using:

Loza M, Teraguchi S, Standley DM, Diez D (2022). “Unbiased integration of single cell transcriptome replicates.” NAR Genomics and Bioinformatics, 1(4), lqac022. doi: 10.1093/nargab/lqac022 (URL: https://doi.org/10.1093/nargab/lqac022).

Installation

You can install the release version of Canek from CRAN with:

install.packages("Canek")

You can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("MartinLoza/Canek")

Example

This is a basic example:

library(Canek)

res <- RunCanek(SimBatches$batches)
res[1:5, 1:5]
#>          Cell1    Cell2    Cell3    Cell4    Cell5
#> Gene1 6.145644 6.228590 6.960904 6.665023 6.586427
#> Gene2 6.919552 7.048549 7.328128 7.649456 7.005002
#> Gene3 5.468337 6.115350 6.146068 6.085750 6.142014
#> Gene4 6.810614 7.076788 6.872226 6.359445 6.303407
#> Gene5 2.848188 2.160687 4.454532 2.467829 3.165861

For more tutorials using Canek check out our github page and vignettes: