To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("EMDomics")

In most cases, you don't need to download the package archive at all.

EMDomics

DOI: 10.18129/B9.bioc.EMDomics    

This is the development version of EMDomics; for the stable release version, see EMDomics.

Earth Mover's Distance for Differential Analysis of Genomics Data

Bioconductor version: Development (3.6)

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.

Author: Sadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi [aut]

Maintainer: Sadhika Malladi <contact at sadhikamalladi.com> and Daniel Schmolze <emd at schmolze.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("EMDomics")

Documentation

HTML R Script EMDomics Vignette
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, Microarray, Software
Version 2.7.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License MIT + file LICENSE
Depends R (>= 3.2.1)
Imports emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package EMDomics_2.7.0.tar.gz
Windows Binary EMDomics_2.7.0.zip
Mac OS X 10.11 (El Capitan) EMDomics_2.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EMDomics
Package Short Url http://bioconductor.org/packages/EMDomics/
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