batchtma

0.2.0

Batch Effect Adjustments

0packages depend

3.7Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Konrad StopsackFirst published 2021-12-062 releasesCRAN page ↗GitHub ↗

Different adjustment methods for batch effects in biomarker data, such as from tissue microarrays. Some methods attempt to retain differences between batches that may be due to between-batch differences in "biological" factors that influence biomarker values.

Install

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

install.packages("batchtma", 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("stopsack/batchtma")

Development version from stopsack/batchtma. 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-batchtma

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

1NOTE12OK

Failing flavors

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

Slowest check: 2.7 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.17

not tracked

Coverage

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 75%

Downloads

3.7K

CRAN downloads in the past year

Rank #11,266 · ~10/day · ~308/mo

Releases R versions

Daily download trend is not available in this view yet.

29130 days

90090 days

3.7K1 year

Compare downloads with other packages →

Also on134 r2u

Repository

GitHub ↗ stopsack/batchtma

1Stars

1Forks

0Open issues

0Open PRs

2Releases

114Commits

3Contributors

batch-effectstissue-microarray-analysismeasurement-error

License GPL-3.0 · 114 commits · Last activity 2026-02-23 · 0% stars, 30d

Stars over time

2023-08-03 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/stopsack/batchtma on 2026-08-02.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

broom dplyr geepack ggplot2 limmannetpurrr quantreg rlang stringr tibble tidyr

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Konrad Stopsack

Author, Maintainer

Authors (2)

Konrad Stopsack

Author, Maintainer

Travis Gerke

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2026-02-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.6
2021-12-06
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-06
Total releases: 2 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 696 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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