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: 2.41.0
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]
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:26:01 UTC
RemoteUrl: https://github.com/bioc/EMDomics
RemoteRef: HEAD
RemoteSha: a487db43774dc92b15d4c73155005b52734cb00b
Packaged: 2026-01-16 21:58:58 UTC; root
Built: R 4.6.0; ; 2026-01-16 22:03:52 UTC; unix
