Package: EMDomics
Title: Earth Mover's Distance for Differential Analysis of Genomics
        Data
Description: 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.
Version: 2.42.0
biocViews: Software, DifferentialExpression, GeneExpression, Microarray
Authors@R: c( person("Sadhika", "Malladi", email="contact@sadhikamalladi.com", role=c("aut","cre")),
        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: Sadhika Malladi <contact@sadhikamalladi.com> and Daniel Schmolze <emd@schmolze.com>
Depends: R (>= 3.2.1)
Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt,
        preprocessCore
Suggests: knitr
License: MIT + file LICENSE
VignetteBuilder: knitr
NeedsCompilation: no
Author: Sadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi
        [aut]
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: RELEASE_3_23
git_last_commit: 127c8f3
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
Packaged: 2026-04-28 21:54:31 UTC; biocbuild
