mdp

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

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("mdp")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")

Running the mdp package	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, Microarray, QualityControl, Software, SystemsBiology, Transcriptomics
Version	1.26.0
In Bioconductor since	BioC 3.7 (R-3.5) (6.5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	ggplot2, gridExtra, grid, stats, utils
System Requirements
URL	https://mdp.sysbio.tools/

Suggests	testthat, knitr, rmarkdown, fgsea, BiocManager
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	mdp_1.26.0.tar.gz
Windows Binary (x86_64)	mdp_1.26.0.zip (64-bit only)
macOS Binary (x86_64)	mdp_1.26.0.tgz
macOS Binary (arm64)	mdp_1.25.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mdp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mdp
Bioc Package Browser	https://code.bioconductor.org/browse/mdp/
Package Short Url	https://bioconductor.org/packages/mdp/
Package Downloads Report	Download Stats