README.md

bbknnR

Use batch balanced KNN (BBKNN) in R

Introduction

BBKNN is a fast and intuitive batch effect removal tool for single-cell data. It is originally used in the scanpy workflow, and now can be used with Seurat seamlessly.

System requirements

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

Installation

bbknnR has been released to CRAN:

install.packages("bbknnR")

or can be installed from github:

devtools::install_github("ycli1995/bbknnR")

Quick start

library(bbknnR)
library(Seurat)
data("panc8_small")
panc8_small <- RunBBKNN(panc8_small, batch_key = "tech")

Release

1.0.2

1.0.1

1.0.0

Citation

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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bbknnR documentation built on Sept. 23, 2022, 1:06 a.m.