mdp

DOI: 10.18129/B9.bioc.mdp    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see mdp.

Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

Bioconductor version: 3.9

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.

Author: Melissa Lever [aut], Pedro Russo [aut], Helder Nakaya [aut, cre]

Maintainer: Helder Nakaya <hnakaya at usp.br>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mdp")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mdp")

 

HTML	R Script	Running the mdp package
PDF		Reference Manual

Details

biocViews	BiomedicalInformatics, Microarray, QualityControl, Software, SystemsBiology, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	GPL-3
Depends	R (>= 3.5)
Imports	ggplot2, gridExtra, grid, stats, utils
LinkingTo
Suggests	testthat, knitr, rmarkdown, fgsea
SystemRequirements
Enhances
URL	https://mdp.sysbio.tools/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mdp_1.4.0.tar.gz
Windows Binary	mdp_1.4.0.zip
Mac OS X 10.11 (El Capitan)	mdp_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mdp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mdp
Package Short Url	https://bioconductor.org/packages/mdp/
Package Downloads Report	Download Stats