CimpleG

1.0.1

A Method to Identify Single CpG Sites for Classification and Deconvolution

0packages depend

2.1Kdownloads / year

19.7%test coverage

13/13checks pass

Overview

About

Maintained by Tiago F.V. MaiéFirst published 2025-12-032 releasesCRAN page ↗GitHub ↗

DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. 'CimpleG' is a method for the detection of small CpG methylation signatures used for cell-type classification and deconvolution. 'CimpleG' is time efficient and performs as well as top performing methods for cell-type classification of blood cells and other somatic cells, while basing its prediction on a single DNA methylation site per cell type (but users can also select more sites if they so wish). Users can train cell type classifiers ('CimpleG' based, and others) and directly apply these in a deconvolution of cell mixes context. Altogether, 'CimpleG' provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution. For more details see Maié et al. (2023) doi:10.1186/s13059-023-03000-0.

Install

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

install.packages("CimpleG", 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("CostaLab/CimpleG")

Development version from CostaLab/CimpleG. 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-cimpleg

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-CimpleG

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

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

Health

CRAN checks

13OK

Slowest check: 9.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.11

19.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 290 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 75%
Documented parameters: 89%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #14,846 · ~6/day · ~171/mo

Releases R versions

Daily download trend is not available in this view yet.

25030 days

75090 days

2.1K1 year

Compare downloads with other packages →

Also on122 r2u

Repository

GitHub ↗ costalab/cimpleg

8Stars

0Forks

0Open issues

0Open PRs

6Releases

255Commits

1Contributors

methylationdeconvolutioncpg-signaturebiomarker-discoverybiomarkerscell-type-classificationr

License GPL-3.0 · 255 commits · Last activity 2025-12-05 · +14.3% stars, 30d

Stars over time

2024-10-15 · 52026-07-07 · 8

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/costalab/cimpleg on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Makefile

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

61 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (37)

archive assertthat broom butcher caret data.table dplyr forcats ggExtra ggplot2 ggrepel ggscigrDevicesgtools magrittr matrixStatsmethodsnnls OneR parsnip patchwork purrr recipes rlang rsample scalesstatstibble tictoc tidyr tidyselect tsutils tuneutilsvroom workflows yardstick

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 5,486 (81%)Rd 1,141 (17%)Vignettes 150 (2%)

Code characteristics

Object systems

S311

Cyclomatic complexity: 2.0 median / 23 max
Test cases: 22 / 0.11 per code line

Test coverage

Line coverage

20%

Expression

23.2%

Tests / Examples

19.7% / – ex

Functions

66 20 exported

Complexity

3.5 avg / 23 max

Call network

66 nodes / 65 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

66 functions

Function	Cyclo	Coverage
darken exp	2	0%
deconv_pred_obs_plot exp	1	0%
deconv_ranking_plot exp	4	0%
deconvolution_barplot exp	4	0%
diffmeans_sumvariance_plot exp	23	0%
dmsv_plot exp	1	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
test_targets	data.frame	170 × 18	–
train_targets	data.frame	409 × 18	–

People & History

People (1)

Maintainer (1)

Tiago F.V. Maié

Author, Maintainer

Authors (1)

Tiago F.V. Maié

Author, Maintainer

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
1.0.1Latest
2025-12-07 · current release · diff ↗
1.0.0
2025-12-03
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-03
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 4.2 MB / 4 files
Download size: 4.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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