CimpleG: A Method to Identify Single CpG Sites for Classification and Deconvolution

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>.

Version:	1.0.0
Depends:	R (≥ 4.1.0)
Imports:	archive, assertthat, broom, butcher, caret, data.table, devtools, dplyr, forcats, ggExtra, ggplot2, ggrepel, ggsci, grDevices, gtools, magrittr, matrixStats, methods, nnls, OneR, parsnip, patchwork, purrr, recipes, rlang, rsample, scales, stats, tibble, tictoc, tidyr, tidyselect, tsutils, tune, utils, vroom, workflows, yardstick
Suggests:	Biobase, biomaRt, C50, circlize, EpiDISH, furrr, future, future.apply, GEOquery, ggbeeswarm, ggsignif, glmnet, knitr, minfi, mltools, NMF, nnet, plyr, ranger, RColorBrewer, reshape2, Rfast, rmarkdown, spelling, stringr, SummarizedExperiment, testthat (≥ 3.0.0), withr, xgboost
Published:	2025-12-03
DOI:	10.32614/CRAN.package.CimpleG (may not be active yet)
Author:	Tiago F.V. Maié [aut, cre]
Maintainer:	Tiago F.V. Maié <tiagomaie at hotmail.com>
BugReports:	https://github.com/CostaLab/CimpleG/issues
License:	GPL (≥ 3)
URL:	https://github.com/CostaLab/CimpleG, https://costalab.github.io/CimpleG/
NeedsCompilation:	no
Language:	en-US
Materials:	README
CRAN checks:	CimpleG results [issues need fixing before 2025-12-18]

Documentation:

Reference manual:	CimpleG.html , CimpleG.pdf
Vignettes:	Generate signatures (source, R code) Quickly save and load (large) objects (source, R code)

Downloads:

Package source:	CimpleG_1.0.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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