mdp

DOI: 10.18129/B9.bioc.mdp    

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

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mdp")

Documentation

HTML R Script Running the mdp package
PDF   Reference Manual

Details

biocViews BiomedicalInformatics, Microarray, QualityControl, Software, SystemsBiology, Transcriptomics
Version 1.0.0
License GPL-3
Depends R (>= 3.5)
Imports ggplot2, grid, stats, utils
LinkingTo
Suggests testthat, knitr, rmarkdown, fgsea
SystemRequirements
Enhances
URL https://mdp.sysbio.tools/
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package mdp_1.0.0.tar.gz
Windows Binary mdp_1.0.0.zip
Mac OS X 10.11 (El Capitan) mdp_1.0.0.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 http://bioconductor.org/packages/mdp/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: