Use batch balanced KNN (BBKNN) in R
bbknnR has been tested on R versions >= 4.1. Please consult the
DESCRIPTION file for more details on required R packages. bbknnR has been tested on Linux platforms
To use the full features of
bbknnR, you also need to install the bbknn python package:
pip install bbknn
bbknnR has been released to CRAN:
or can be installed from github:
library(bbknnR) library(Seurat) data("panc8_small") panc8_small <- RunBBKNN(panc8_small, batch_key = "tech")
compute_connectivities_umap()to follow the CRAN policy
Please cite this implementation R in if you use it:
Yuchen Li (2022). bbknnR: Use batch balanced KNN (BBKNN) in R. package version 0.1.0 https://github.com/ycli1995/bbknnR
Please also cite the original publication of this algorithm.
Polanski, Krzysztof, et al. "BBKNN: fast batch alignment of single cell transcriptomes." Bioinformatics 36.3 (2020): 964-965.
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