[bug#54790] [PATCH 0/3] Add r-copykat and dependencies

[bug#54790] [PATCH 0/3] Add r-copykat and dependencies

[zimoun]

Hi,

I hope that all is fine.


Cheers,
simon

zimoun (3):
  gnu: Add r-paralleldist.
  gnu: Add r-dlm.
  gnu: Add r-copykat.

 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++
 gnu/packages/cran.scm           | 53 +++++++++++++++++++++++++++++++++
 2 files changed, 91 insertions(+)


base-commit: 09ec1d65613e111a3ee2cbeda350441e058deb8f
-- 
2.34.0

[bug#54790] [PATCH 1/3] gnu: Add r-paralleldist.

[zimoun]

* gnu/packages/cran.scm (r-paralleldist): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index be77a57f28..b9ea1144f2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1074,6 +1074,39 @@ (define-public r-pacman
 functions which can speed up workflow.")
     (license license:gpl2)))
 
+(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+)))
+
 (define-public r-pheatmap
   (package
     (name "r-pheatmap")
-- 
2.34.0

[bug#54790] [PATCH 2/3] gnu: Add r-dlm.

[zimoun]

* gnu/packages/cran.scm (r-dlm): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b9ea1144f2..5a852af4b7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -659,6 +659,26 @@ (define-public r-clipr
 the system clipboards.")
     (license license:gpl3)))
 
+(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+)))
+
 (define-public r-zoo
   (package
     (name "r-zoo")
-- 
2.34.0

[bug#54790] [PATCH 3/3] gnu: Add r-copykat.

[zimoun]

* gnu/packages/bioinformatics.scm (r-copykat): New variable.
---
 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 106b25a50b..e3cca9aab8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9138,6 +9138,44 @@ (define-public r-cellchat
 communication networks from scRNA-seq data.")
       (license license:gpl3))))
 
+(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))))
+
 (define-public sambamba
   (package
     (name "sambamba")
-- 
2.34.0

bug#54790: [PATCH 0/3] Add r-copykat and dependencies

[Ricardo Wurmus]

Thank you for the patches!

> zimoun (3):
>   gnu: Add r-paralleldist.
>   gnu: Add r-dlm.
>   gnu: Add r-copykat.

I shortened the description of r-paralleldist and pushed the three
patches.

-- 
Ricardo