mdp
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
DOI: 10.18129/B9.bioc.mdp
Bioconductor version: Release (3.19)
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("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 |
Details
| biocViews | BiomedicalInformatics, Microarray, QualityControl, Software, SystemsBiology, Transcriptomics |
| Version | 1.24.0 |
| 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/ |
See More
| 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | mdp_1.24.0.zip |
| macOS Binary (x86_64) | mdp_1.24.0.tgz |
| macOS Binary (arm64) | mdp_1.24.0.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 |