Package: mdp
Title: Molecular Degree of Perturbation calculates scores for
        transcriptome data samples based on their perturbation from
        controls
Version: 1.31.0
Authors@R: c(person("Melissa", "Lever", email = "melissalever@gmail.com", role = c("aut")), person("Pedro", "Russo", email = "pedro.russo@usp.br", role = c("aut")),
            person("Helder", "Nakaya", email = "hnakaya@usp.br", role = c("aut", "cre")))
Description: The Molecular Degree of Perturbation webtool quantifies
        the heterogeneity of samples. It takes a data.frame of omic
        data that contains at least two classes (control and test) and
        assigns a score to all samples based on how perturbed they are
        compared to the controls. It is based on the Molecular Distance
        to Health (Pankla et al. 2009), and expands on this algorithm
        by adding the options to calculate the z-score using the
        modified z-score (using median absolute deviation), change the
        z-score zeroing threshold, and look at genes that are most
        perturbed in the test versus control classes.
URL: https://mdp.sysbio.tools/
biocViews: BiomedicalInformatics, QualityControl, Transcriptomics,
        SystemsBiology, Microarray, QualityControl
Depends: R (>= 4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: ggplot2, gridExtra, grid, stats, utils
Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager
VignetteBuilder: knitr
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:44:58 UTC
RemoteUrl: https://github.com/bioc/mdp
RemoteRef: HEAD
RemoteSha: d77d61e62b6b87f7df148b0eaf4c5ddd372d035c
NeedsCompilation: no
Packaged: 2026-01-25 07:59:29 UTC; root
Author: Melissa Lever [aut],
  Pedro Russo [aut],
  Helder Nakaya [aut, cre]
Maintainer: Helder Nakaya <hnakaya@usp.br>
Built: R 4.6.0; ; 2026-01-25 08:00:52 UTC; windows
