Package: DeCovarT
Title: Covariance-Aware Deconvolution of Bulk Transcriptomic Samples
Version: 2.3.1
Authors@R: 
    person("Bastien", "Chassagnol", , "bastien_chassagnol@laposte.net", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8955-2391"))
Description: Estimates cell-type proportions in bulk transcriptomic
        samples with a probabilistic convolution model that integrates
        the gene-gene covariance structure of purified reference
        profiles. Cellular ratios are recovered by maximum likelihood
        under a multivariate Gaussian convolution, using analytic
        gradients and Hessians, an isometric log-ratio
        reparametrisation (Helmert basis) that enforces the simplex
        constraint, and Marquardt-Levenberg or Newton-type optimisers.
        The methodology is described in Chassagnol, Nuel and Becht
        (2023) <doi:10.48550/arXiv.2309.09557>.
License: MIT + file LICENSE
URL: https://github.com/bastienchassagnol/DeCovarT,
        https://bastienchassagnol.github.io/DeCovarT/
BugReports: https://github.com/bastienchassagnol/DeCovarT/issues
Depends: R (>= 4.1.0)
Imports: dplyr, ggplot2 (>= 3.5.0), marqLevAlg, MASS, Matrix, purrr,
        Rdpack (>= 0.7), rlang, tensor, tibble, tidyr
Suggests: circlize, cli, ComplexHeatmap, compositions, cowplot, e1071,
        EMMIXmfa, flextable, forcats, funkyheatmap, furrr, future,
        ggdendro, ggdist, ggtext, glmnet, gridExtra, htmlwidgets,
        igraph, knitr, limSolve, litedown, mclust, Metrics, MixSim,
        mvtnorm, nnls, numDeriv, patchwork, pkgdown, plotly, png, ps,
        qrng, quarto, qqplotr, reactable (>= 0.4.4), readr, rgl,
        rmarkdown, spelling, stringr, testthat (>= 3.0.0), tinytable
        (>= 0.15.0), viridis, withr
VignetteBuilder: knitr, quarto
RdMacros: Rdpack
Config/roxygen2/version: 8.1.0
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd",
        "srr::srr_stats_roclet"))
RoxygenNote: 8.1.0
Config/pak/sysreqs: libicu-dev
Repository: https://bastienchassagnol.r-universe.dev
Date/Publication: 2026-10-01 15:38:11 UTC
RemoteUrl: https://github.com/bastienchassagnol/DeCovarT
RemoteRef: HEAD
RemoteSha: 5245f2cf91276ed01a14d60aa4944ef0fcf58e54
NeedsCompilation: no
Packaged: 2026-10-01 20:06:32 UTC; root
Author: Bastien Chassagnol [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8955-2391>)
Maintainer: Bastien Chassagnol <bastien_chassagnol@laposte.net>