new packages: r-scdblfinder and dependencies (#32367)

- r-bluster
- r-metapod
- r-scran

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"))