Package: idiffomix
Type: Package
Title: Integrated Differential Analysis of Multi Omics Data using a
        Joint Mixture Model
Version: 1.0.0
Authors@R: c(person("Koyel","Majumdar",email="koyelmajumdar.phdresearch@gmail.com",
        role=c("cre","aut")),
        person("Isobel Claire","Gorley",email="claire.gormley@ucd.ie",
        role="aut"),
        person("Thomas Brendan","Murphy",email="brendan.murphy@ucd.ie", 
        role="aut"),
        person("Florence","Jaffrezic",email="florence.jaffrezic@inrae.fr",
        role="aut"),
        person("Andrea","Rau",email="andrea.rau@inrae.fr",role="aut"))
Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>
Description: A joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: foreach, doParallel, parallel, mclust, stats, utils, edgeR,
        magrittr, ggplot2, scales, tidyr, dplyr, reshape2, gridExtra,
        grid, tidyselect, cowplot
Encoding: UTF-8
NeedsCompilation: yes
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Packaged: 2025-01-10 10:22:28 UTC; koyel
Author: Koyel Majumdar [cre, aut],
  Isobel Claire Gorley [aut],
  Thomas Brendan Murphy [aut],
  Florence Jaffrezic [aut],
  Andrea Rau [aut]
Repository: CRAN
Date/Publication: 2025-01-13 17:20:02 UTC
Built: R 4.6.0; ; 2026-04-25 23:27:17 UTC; unix
