bbknnR

2.0.2

Perform Batch Balanced KNN in R

0packages depend

7.4Kdownloads / year

66.7%test coverage

12/13checks pass

Overview

About

Maintained by Yuchen LiFirst published 2022-05-278 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bbknnR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ycli1995/bbknnR")

Development version from ycli1995/bbknnR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bbknnr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bbknnR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bbknnR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.3 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.10

66.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 246 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

7.4K

CRAN downloads in the past year

Rank #5,156 · ~20/day · ~616/mo

Releases R versions

Daily download trend is not available in this view yet.

32030 days

1.6K90 days

7.4K1 year

Compare downloads with other packages →

Also on478 r2u11 autocran

Repository

GitHub ↗ ycli1995/bbknnr

14Stars

5Forks

5Open issues

0Open PRs

0Releases

21Commits

2Contributors

21 commits · Last activity 2025-09-09 · 0% stars, 30d

Stars over time

2025-07-16 · 112026-07-07 · 14

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/ycli1995/bbknnr on 2026-08-02.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.1.0methodsutils

Imports (13)

future future.apply glmnet Rcpp RcppAnnoy RcppEigen rlang rnndescent Rtsne Seurat SeuratObject tidytable uwot

LinkingTo (2)

Rcpp RcppEigen

Suggests (5)

dplyr knitr rmarkdown testthat patchwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Yuchen Li

Author, Maintainer

Authors (1)

Yuchen Li

Author, Maintainer

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.0.2Latest
2025-09-10 · current release · diff ↗
2.0.1
2025-06-05 · diff ↗
2.0.0
2025-06-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.1
2024-02-13 · diff ↗
1.1.0
2023-11-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.2
2022-09-23 · diff ↗
1.0.1
2022-08-23 · diff ↗
1.0.0
2022-05-27
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-27
Total releases: 8 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.3 MB / 1 file
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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