# Copyright 2013-2023 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 RVsn(RPackage):
    """Variance stabilization and calibration for microarray data.

    The package implements a method for normalising microarray intensities,
    and works for single- and multiple-color arrays. It can also be used for
    data from other technologies, as long as they have similar format. The
    method uses a robust variant of the maximum-likelihood estimator for an
    additive-multiplicative error model and affine calibration. The model
    incorporates data calibration step (a.k.a. normalization), a model for
    the dependence of the variance on the mean intensity and a variance
    stabilizing data transformation. Differences between transformed
    intensities are analogous to "normalized log-ratios". However, in
    contrast to the latter, their variance is independent of the mean, and
    they are usually more sensitive and specific in detecting differential
    transcription."""

    bioc = "vsn"

    version("3.68.0", commit="b8c9cef9730a00a810e8ec08e472b26d0bff5357")
    version("3.66.0", commit="ddccd6c74ebea426056794c2bfad2dfd02631092")
    version("3.64.0", commit="1f09f20ee7f81100fb0bf66288c4caf0049b5508")
    version("3.62.0", commit="6ae7f4e07ec1a5a9482cab892d98175983bfcd50")
    version("3.58.0", commit="a451e6ae989623750feacf26d99683a7955adf85")
    version("3.52.0", commit="e80642d850ae93bc141654200a8970b561a94fbe")
    version("3.50.0", commit="ad49fcc288c6065d0f04040acd688e7f0d7d927e")
    version("3.48.1", commit="d57f64112004b1d73b3be625949830209de027eb")
    version("3.46.0", commit="7ecfd20452348da27d6fcc052cbff2b9be777792")
    version("3.44.0", commit="e54513fcdd07ccfb8094359e93cef145450f0ee0")

    depends_on("r@3.0.0:", type=("build", "run"))
    depends_on("r@3.4.0:", type=("build", "run"), when="@3.46.0:")
    depends_on("r@4.0.0:", type=("build", "run"), when="@3.62.0:")
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-affy", type=("build", "run"))
    depends_on("r-limma", type=("build", "run"))
    depends_on("r-lattice", type=("build", "run"))
    depends_on("r-ggplot2", type=("build", "run"))

    depends_on("r-hexbin", type=("build", "run"), when="@3.44.0:3.52.0")