Package: EMDomics
Title: Earth Mover's Distance for Differential Analysis of Genomics
        Data
Description: The EMDomics algorithm is used to perform a supervised
        two-class analysis to measure the magnitude and statistical
        significance of observed continuous genomics data between two
        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 two 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 the other, 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.
Version: 1.0.0
biocViews: Software, DifferentialExpression, GeneExpression, Microarray
Authors@R: c( person("Daniel", "Schmolze", email="emd@schmolze.com",
        role=c("aut", "cre")), person("Andrew", "Beck",
        email="abeck2@bidmc.harvard.edu", role="aut"), person("Sheida",
        "Nabavi", email="sheida_nabavi@hms.harvard.edu", role="aut"))
Maintainer: Daniel Schmolze <emd@schmolze.com>
Depends: R (>= 3.2.0)
Imports: emdist, BiocParallel, matrixStats, ggplot2
Suggests: knitr
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Author: Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi
        [aut]
Packaged: 2015-04-17 06:01:36 UTC; biocbuild
Built: R 3.2.0; ; 2015-04-17 08:29:57 UTC; windows
