# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class RTmixclust(RPackage):
    """Time Series Clustering of Gene Expression with Gaussian Mixed-Effects
    Models and Smoothing Splines.

    Implementation of a clustering method for time series gene expression
    data based on mixed-effects models with Gaussian variables and non-
    parametric cubic splines estimation. The method can robustly account for
    the high levels of noise present in typical gene expression time series
    datasets."""

    bioc = "TMixClust"

    version("1.22.0", commit="bb750ce4682542ba8e2cb5bfbdb5eff839ffacd4")
    version("1.20.0", commit="df27f53d088b02cf596504b44909f2762900ab49")
    version("1.18.0", commit="71f80a7ace481f46471f36c91223effb85e17186")
    version("1.16.0", commit="e525cfd9c729a73a1964c243e5c34c37343f7bfa")
    version("1.12.0", commit="982b31bd7e22a3dc638bbda0336546220444f0c2")
    version("1.6.0", commit="9f5f78e52538d15f402c8f6e4c60f7212c7bc548")
    version("1.4.0", commit="a52fcae6e7a5dd41e7afbe128f35397e8bc8cb12")
    version("1.2.0", commit="0250c0b238f08077b5b9ff17c2f3b7633c67dc3c")
    version("1.0.1", commit="0ac800210e3eb9da911767a80fb5582ab33c0cad")

    depends_on("r@3.4:", type=("build", "run"))
    depends_on("r-gss", type=("build", "run"))
    depends_on("r-mvtnorm", type=("build", "run"))
    depends_on("r-zoo", type=("build", "run"))
    depends_on("r-cluster", type=("build", "run"))
    depends_on("r-biocparallel", type=("build", "run"))
    depends_on("r-flexclust", type=("build", "run"))
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-spem", type=("build", "run"))