R Observatory: Metrics for ACNE version 0.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ACNE

0.9.2

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

0packages depend

4.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Henrik BengtssonFirst published 2011-09-168 releasesCRAN page ↗GitHub ↗

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Latest changes · 0.9.2

Install

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

install.packages("ACNE", 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("HenrikBengtsson/ACNE")

Development version from HenrikBengtsson/ACNE. 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-acne

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

13OK

Slowest check: 2.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-13
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-12
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 · 80 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 21%

Downloads

4.4K

CRAN downloads in the past year

Rank #7,982 · ~12/day · ~364/mo

Releases R versions

Daily download trend is not available in this view yet.

34730 days

1.1K90 days

4.4K1 year

Compare downloads with other packages →

Also on141 r2u

Repository

GitHub ↗ henrikbengtsson/acne

0Stars

0Forks

1Open issues

0Open PRs

0Releases

rpackagecran

Last activity 2025-08-19

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/henrikbengtsson/acne on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0.0aroma.affymetrix

Imports (7)

MASSR.methodsS3 R.oo R.utils (>= 2.1.0)matrixStats R.filesets aroma.core

LinkingTo (0)

none

Suggests (1)

DNAcopy

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Authors (3)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Maria Ortiz

Author

Angel Rubio

Author

Copyright holders (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder

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
0.9.2Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.9.1
2024-02-17 · diff ↗
0.9.0
2023-06-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.8.1
2015-10-27 · diff ↗
R
R 3.2.0 released · 2015-04-16

Show 9 earlier events

0.8.0
2015-02-23 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.7.0
2013-10-19 · diff ↗
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.5.0
2011-10-25 · diff ↗
0.4.3
2011-09-16
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-09-16
Total releases: 8 / 15 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.0.0
Download size: 61 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ACNE")

Format

Bengtsson, H., Ortiz, M., & Rubio, A. (2025). ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization (Version 0.9.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ACNE

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ACNE version 0.9.2 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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