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# 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 RSnprelate(RPackage):
"""Parallel Computing Toolset for Relatedness and Principal Component
Analysis of SNP Data.
Genome-wide association studies (GWAS) are widely used to investigate
the genetic basis of diseases and traits, but they pose many
computational challenges. We developed an R package SNPRelate to provide
a binary format for single-nucleotide polymorphism (SNP) data in GWAS
utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS
format offers the efficient operations specifically designed for
integers with two bits, since a SNP could occupy only two bits.
SNPRelate is also designed to accelerate two key computations on SNP
data using parallel computing for multi-core symmetric multiprocessing
computer architectures: Principal Component Analysis (PCA) and
relatedness analysis using Identity-By-Descent measures. The SNP GDS
format is also used by the GWASTools package with the support of S4
classes and generic functions. The extended GDS format is implemented in
the SeqArray package to support the storage of single nucleotide
variations (SNVs), insertion/deletion polymorphism (indel) and
structural variation calls."""
bioc = "SNPRelate"
version("1.34.0", commit="27a7c9658b974f9887f48a4a3ed1a7621b141488")
version("1.32.0", commit="2e8cc807baa74fca5137148b672f3945c36689b2")
version("1.30.1", commit="baef8a71d3908287a2307768348c02db0720d125")
version("1.28.0", commit="8fcd837f4627a3bb77cb8d992b2baedd0589d123")
version("1.24.0", commit="419b13b761ea39a8b1b9bc73097fb0359c59f1c2")
version("1.18.1", commit="81c581bf76392efdc8ba237ca2e42ca1dba788ca")
version("1.16.0", commit="0e38e8df4af87dff6c27a23af2867661998c0d85")
version("1.14.0", commit="9501cbfc411aa320e58654a865fda2e9077977af")
version("1.12.2", commit="dce2e2b6f36483a9f905bb5df6ae834a9f1136fe")
version("1.10.2", commit="3f5c4010871df742e7a460586b38ad0c2fd37aeb")
depends_on("r@2.15:", type=("build", "run"))
depends_on("r-gdsfmt@1.8.3:", type=("build", "run"))
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