Package: bbknnR 2.0.2

bbknnR: Perform Batch Balanced KNN in R

A fast and intuitive batch effect removal tool for single-cell data. BBKNN is originally used in the 'scanpy' python package, and now can be used with 'Seurat' seamlessly.

Authors:Yuchen Li [aut, cre]

bbknnR_2.0.2.tar.gz
bbknnR_2.0.2.zip(r-4.7-x86_64)bbknnR_2.0.2.zip(r-4.7-arm64)bbknnR_2.0.2.zip(r-4.6-x86_64)bbknnR_2.0.2.zip(r-4.6-arm64)bbknnR_2.0.2.zip(r-4.5-x86_64)
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bbknnR_2.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bbknnR/json (API)

# Install 'bbknnR' in R:

install.packages('bbknnR', repos = c('https://ycli1995.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ycli1995/bbknnr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

panc8_small - A small example version of the pancreas scRNA-seq dataset

On CRAN:

cpp

5.42 score 14 stars 38 scripts 654 downloads 2 exports 149 dependencies

Last updated from:6b7a823223. Checks:13 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	271
linux-devel-x86_64	WARNING	311
source / vignettes	OK	317
linux-release-arm64	WARNING	258
linux-release-x86_64	WARNING	283
macos-release-arm64	WARNING	272
macos-release-x86_64	WARNING	368
macos-oldrel-arm64	WARNING	374
macos-oldrel-x86_64	WARNING	725
windows-devel-arm64	WARNING	463
windows-devel-x86_64	WARNING	301
windows-release-arm64	WARNING	514
windows-release-x86_64	WARNING	238
windows-oldrel-x86_64	WARNING	287
wasm-release	OK	167

Exports:RidgeRegression RunBBKNN

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics ggplot2 ggrepel ggridges glmnet globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppThread RcppTOML reshape2 reticulate rlang rmarkdown rnndescent ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shape shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tidytable tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

bbknnR Tutorial

Setup library and data | Run BBKNN | Find Clusters using bbknn graph | Visualization

Rendered frombbknnR-tutorial.Rmdusingknitr::rmarkdown

Last update: 2025-06-03
Started: 2022-05-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A small example version of the pancreas scRNA-seq dataset	panc8_small
Perform ridge regression on scaled expression data	RidgeRegression RidgeRegression.default RidgeRegression.Seurat
Perform batch balanced KNN	RunBBKNN RunBBKNN.matrix RunBBKNN.Seurat