Type: Package
Package: CimpleG
Title: A Method to Identify Single CpG Sites for Classification and
        Deconvolution
Version: 1.0.1
Date: 2025-11-21
Authors@R: 
    person("Tiago", "F.V. Maié", , "tiagomaie@hotmail.com", role = c("aut", "cre"))
Maintainer: Tiago F.V. Maié <tiagomaie@hotmail.com>
Description: 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>.
License: GPL (>= 3)
URL: https://github.com/CostaLab/CimpleG,
        https://costalab.github.io/CimpleG/
BugReports: https://github.com/CostaLab/CimpleG/issues
Depends: R (>= 4.1.0)
Imports: archive, assertthat, broom, butcher, caret, data.table, 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
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-12-05 17:19:43 UTC; tmaie
Author: Tiago F.V. Maié [aut, cre]
Repository: CRAN
Date/Publication: 2025-12-07 00:50:19 UTC
Built: R 4.4.3; ; 2026-01-12 22:09:54 UTC; windows
