[PATCH 0/3] Add r-copykat and dependencies

+++ b/gnu/packages/cran.scm

+(define-public r-paralleldist

+  (package

+    (name "r-paralleldist")

+    (version "0.2.6")

+    (source

+     (origin

+       (method url-fetch)

+       (uri (cran-uri "parallelDist" version))

+       (sha256

+        (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))

+    (properties `((upstream-name . "parallelDist")))

+    (build-system r-build-system)

+    (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))

+    (home-page "https://github.com/alexeckert/parallelDist")

+    (synopsis "Parallel Distance Matrix Computation using Multiple Threads")

+    (description

+     "This package provides a fast parallelized alternative to R's native

+'dist' function to calculate distance matrices for continuous, binary, and

+multi-dimensional input matrices, which supports a broad variety of 41

+predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages,

+as well as user- defined functions written in C++.  For ease of use, the

+'parDist' function extends the signature of the 'dist' function and uses the

+same parameter naming conventions as distance methods of existing R packages.

+The package is mainly implemented in C++ and leverages the 'RcppParallel'

+package to parallelize the distance computations with the help of the

+'TinyThread' library.  Furthermore, the 'Armadillo' linear algebra library is

+used for optimized matrix operations during distance calculations.  The

+curiously recurring template pattern (CRTP) technique is applied to avoid

+virtual functions, which improves the Dynamic Time Warping calculations while

+the implementation stays flexible enough to support different DTW step

+patterns and normalization methods.")

+    (license license:gpl2+)))

+

+++ b/gnu/packages/cran.scm

+(define-public r-dlm

+  (package

+    (name "r-dlm")

+    (version "1.1-5")

+    (source

+     (origin

+       (method url-fetch)

+       (uri (cran-uri "dlm" version))

+       (sha256

+        (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))

+    (properties `((upstream-name . "dlm")))

+    (build-system r-build-system)

+    (home-page "https://cran.r-project.org/package=dlm")

+    (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")

+    (description

+     "This package provides routines for Maximum likelihood, Kalman filtering

+and smoothing, and Bayesian analysis of Normal linear State Space models, also

+known as Dynamic Linear Models.")

+    (license license:gpl2+)))

+

+++ b/gnu/packages/bioinformatics.scm

+(define-public r-copykat

+  (let ((commit                         ;no tag

+         "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53")

+        (revision "0"))

+    (package

+      (name "r-copykat")

+      (version (git-version "1.0.8" revision commit))

+      (source

+       (origin

+         (method git-fetch)

+         (uri (git-reference

+               (url "https://github.com/navinlabcode/copykat")

+               (commit commit)))

+         (file-name (git-file-name name version))

+         (sha256

+          (base32

+           "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8"))))

+      (properties `((upstream-name . "copykat")))

+      (build-system r-build-system)

+      (propagated-inputs

+       (list r-cluster

+             r-dlm

+             r-gplots

+             r-mcmcpack

+             r-mixtools

+             r-paralleldist

+             r-rcolorbrewer))

+      (native-inputs (list r-knitr))

+      (home-page "https://github.com/navinlabcode/copykat")

+      (synopsis "Inference of genomic copy number from single cell RNAseq data")

+      (description

+       "This package Copynumber KAryotyping of Tumors infers genomic copy

+number and subclonal structure of human tumors using integrative Bayesian

+approaches to identify genome-wide aneuploidy at 5MB resolution in single

+cells data.  It separates tumor cells and tumor subclones from normal cells

+using high-throughput sc-RNAseq data.")

+      (license license:gpl2))))

+