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Diffstat (limited to 'var')
4 files changed, 134 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-bluster/package.py b/var/spack/repos/builtin/packages/r-bluster/package.py new file mode 100644 index 0000000000..7b31b4e185 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bluster/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2022 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 RBluster(RPackage): + """Clustering Algorithms for Bioconductor. + + Wraps common clustering algorithms in an easily extended S4 framework. + Backends are implemented for hierarchical, k-means and graph-based + clustering. Several utilities are also provided to compare and evaluate + clustering results.""" + + bioc = "bluster" + + version("1.6.0", commit="ff86c7d8d36233e838d4f00e6a4e173e7bf16816") + + depends_on("r-cluster", type=("build", "run")) + depends_on("r-matrix", type=("build", "run")) + depends_on("r-rcpp", type=("build", "run")) + depends_on("r-igraph", type=("build", "run")) + depends_on("r-s4vectors", type=("build", "run")) + depends_on("r-biocparallel", type=("build", "run")) + depends_on("r-biocneighbors", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-metapod/package.py b/var/spack/repos/builtin/packages/r-metapod/package.py new file mode 100644 index 0000000000..b3759f931b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-metapod/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2022 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 RMetapod(RPackage): + """Meta-Analyses on P-Values of Differential Analyses. + + Implements a variety of methods for combining p-values in differential + analyses of genome-scale datasets. Functions can combine p-values across + different tests in the same analysis (e.g., genomic windows in ChIP-seq, + exons in RNA-seq) or for corresponding tests across separate analyses + (e.g., replicated comparisons, effect of different treatment conditions). + Support is provided for handling log-transformed input p-values, missing + values and weighting where appropriate.""" + + bioc = "metapod" + + version("1.4.0", commit="e71c2072e5b39f74599e279b28f4da7923b515fb") + + depends_on("r-rcpp", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-scdblfinder/package.py b/var/spack/repos/builtin/packages/r-scdblfinder/package.py new file mode 100644 index 0000000000..2dcd41c257 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scdblfinder/package.py @@ -0,0 +1,42 @@ +# Copyright 2013-2022 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 RScdblfinder(RPackage): + """The scDblFinder package gathers various methods for the detection and + handling of doublets/multiplets in single-cell sequencing data (i.e. + multiple cells captured within the same droplet or reaction volume). It + includes methods formerly found in the scran package, the new fast and + comprehensive scDblFinder method, and a reimplementation of the Amulet + detection method for single-cell ATAC-seq.""" + + bioc = "scDblFinder" + + version("1.10.0", commit="03512cad0cdfe3cddbef66ec5e330b53661eccfc") + + depends_on("r@4.0:", type=("build", "run")) + depends_on("r-igraph", type=("build", "run")) + depends_on("r-matrix", type=("build", "run")) + depends_on("r-biocgenerics", type=("build", "run")) + depends_on("r-biocparallel", type=("build", "run")) + depends_on("r-biocneighbors", type=("build", "run")) + depends_on("r-biocsingular", type=("build", "run")) + depends_on("r-s4vectors", type=("build", "run")) + depends_on("r-summarizedexperiment", type=("build", "run")) + depends_on("r-singlecellexperiment", type=("build", "run")) + depends_on("r-scran", type=("build", "run")) + depends_on("r-scater", type=("build", "run")) + depends_on("r-scuttle", type=("build", "run")) + depends_on("r-bluster", type=("build", "run")) + depends_on("r-delayedarray", type=("build", "run")) + depends_on("r-xgboost", type=("build", "run")) + depends_on("r-mass", type=("build", "run")) + depends_on("r-iranges", type=("build", "run")) + depends_on("r-genomicranges", type=("build", "run")) + depends_on("r-genomeinfodb", type=("build", "run")) + depends_on("r-rsamtools", type=("build", "run")) + depends_on("r-rtracklayer", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-scran/package.py b/var/spack/repos/builtin/packages/r-scran/package.py new file mode 100644 index 0000000000..fcf4f46534 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scran/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2022 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 RScran(RPackage): + """Methods for Single-Cell RNA-Seq Data Analysis. + + Implements miscellaneous functions for interpretation of single-cell + RNA-seq data. Methods are provided for assignment of cell cycle phase, + detection of highly variable and significantly correlated genes, + identification of marker genes, and other common tasks in routine + single-cell analysis workflows.""" + + bioc = "scran" + + version("1.24.0", commit="c3f9e169c4538ce827d4f14a4141571c2366cd31") + + depends_on("r-singlecellexperiment", type=("build", "run")) + depends_on("r-scuttle", type=("build", "run")) + depends_on("r-summarizedexperiment", type=("build", "run")) + depends_on("r-s4vectors", type=("build", "run")) + depends_on("r-biocgenerics", type=("build", "run")) + depends_on("r-biocparallel", type=("build", "run")) + depends_on("r-rcpp", type=("build", "run")) + depends_on("r-matrix", type=("build", "run")) + depends_on("r-edger", type=("build", "run")) + depends_on("r-limma", type=("build", "run")) + depends_on("r-igraph", type=("build", "run")) + depends_on("r-statmod", type=("build", "run")) + depends_on("r-delayedarray", type=("build", "run")) + depends_on("r-delayedmatrixstats", type=("build", "run")) + depends_on("r-biocsingular", type=("build", "run")) + depends_on("r-bluster", type=("build", "run")) + depends_on("r-metapod", type=("build", "run")) + depends_on("r-dqrng", type=("build", "run")) + depends_on("r-beachmat", type=("build", "run")) + depends_on("r-bh", type=("build", "run")) |