Canek

0.3.1

Batch Correction of Single Cell Transcriptome Data

0packages depend

3.2Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Martin LozaFirst published 2022-03-237 releasesCRAN page ↗GitHub ↗

Non-linear/linear hybrid method for batch-effect correction that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) doi:10.1093/nargab/lqac022.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Canek", 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("MartinLoza/Canek")

Development version from MartinLoza/Canek. 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-canek

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

Health

CRAN checks

1ERROR1NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-arm64

Slowest check: 7.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.31

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-07-18
12 OK · 0 NOTE · 0 WARNING · 1 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
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 2 earlier snapshots

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 526 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.2K

CRAN downloads in the past year

Rank #10,915 · ~9/day · ~268/mo

Releases R versions

Daily download trend is not available in this view yet.

27030 days

92190 days

3.2K1 year

Compare downloads with other packages →

Also on202 r2u

Repository

GitHub ↗ martinloza/canek

7Stars

1Forks

1Open issues

0Open PRs

1Releases

523Commits

6Contributors

rsingle-cell-rna-seqtranscriptomicsbatch-effectsbioinformatics

523 commits · Last activity 2026-07-17 · 0% stars, 30d

Stars over time

2024-04-16 · 42026-07-07 · 7

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/martinloza/canek on 2026-08-02.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

FNN irlba numbers fpc bluster igraph matrixStatsmethodsparallelutils

LinkingTo (0)

none

Suggests (11)

testthat Seurat SingleCellExperiment SummarizedExperiment scater batchelor scran knitr rmarkdown patchwork ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Martin Loza

Author, Maintainer

Authors (2)

Martin Loza

Author, Maintainer

Diego Diez

Author

Package Timeline

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

0.3.1Latest
2026-07-18 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.5
2023-12-08 · diff ↗
0.2.4
2023-11-06 · diff ↗
0.2.3
2023-10-18 · diff ↗
0.2.2
2023-05-31 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.1
2022-05-10 · diff ↗
unarchivedReturned to CRAN
2022-05-10
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-04-15
installation issues were not corrected in time
0.2.0
2022-03-23
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-23
Total releases: 7 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.3 MB / 1 file
Download size: 2.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →