[bug#59840] [PATCH] gnu: Add r-clustercrit, .r-waffle and r-amplican.

[bug#59840] [PATCH] gnu: Add r-clustercrit, .r-waffle and r-amplican.

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 130 bytes --]

* gnu/packages/cran.scm (r-clustercrit, r-waffle): New variables.

* gnu/packages/bioconductor.scm (r-amplican): New variable.

[-- Attachment #2: Type: text/html, Size: 567 bytes --]

[bug#59840] [PATCH 1/3] gnu: Add r-clustercrit.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-clustercrit): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c5258d6e0..6c2b8c834b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14094,6 +14094,30 @@ (define-public r-npsurv
 exact and interval-censored observations.")
     (license license:gpl2+)))
 
+(define-public r-clustercrit
+  (package
+    (name "r-clustercrit")
+    (version "1.2.8")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "clusterCrit" version))
+              (sha256
+               (base32
+                "10pz1bikdbkm2ky3xnagp0qv60whalavp6j39b4p7d75jj5xcxgk"))))
+    (properties `((upstream-name . "clusterCrit")))
+    (build-system r-build-system)
+    (native-inputs (list gfortran))
+    (home-page "https://www.r-project.org/")
+    (synopsis "Computing clustering validation indices")
+    (description
+     "The @code{clusterCrit} package provides an implementation of the following
+indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, McNemar, Kulczynski,
+Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath.  ClusterCrit defines
+several functions which compute internal quality indices or external comparison
+indices.  The partitions are specified as an integer vector giving the index of
+the cluster each observation belongs to.")
+    (license license:gpl2+)))
+
 (define-public r-clusteval
   (package
     (name "r-clusteval")

base-commit: b2a848d23d37f31496e1ff664f1dcf6abcdcc388
-- 
2.38.1

[bug#59840] [PATCH 2/3] gnu: Add r-waffle.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-waffle): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6c2b8c834b..33c2a59d25 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15146,6 +15146,35 @@ (define-public r-tm
      "This package provides a framework for text mining applications within R.")
     (license license:gpl3)))
 
+(define-public r-waffle
+  (package
+    (name "r-waffle")
+    (version "0.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "waffle" version))
+              (sha256
+               (base32
+                "1qjmai33p96cyavi9lgi6k30h6fj7db5sr569v9jf4kwx92c61df"))))
+    (properties `((upstream-name . "waffle")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-extrafont
+           r-ggplot2
+           r-gridextra
+           r-gtable
+           r-rcolorbrewer))
+    (home-page "https://github.com/hrbrmstr/waffle/tree/cran")
+    (synopsis "Creating waffle chart visualizations in R")
+    (description
+     "This package creates square pie charts also known as waffle charts.  These
+can be used to communicate parts of a whole for categorical quantities.  To emulate
+the percentage view of a pie chart, a 10x10 grid should be used.  In this way each
+square is representing 1% of the total.  @code{Waffle} provides tools to create
+charts as well as stitch them together.  Isotype pictograms can be made by using
+glyphs.")
+    (license license:gpl2+)))
+
 (define-public r-waveslim
   (package
     (name "r-waveslim")
-- 
2.38.1

[bug#59840] [PATCH 3/3] gnu: Add r-amplican.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-amplican): New variable.
---
 gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c62c5970b8..7e92186505 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2178,6 +2178,52 @@ (define-public r-airpart
 datasets.")
     (license license:gpl2)))
 
+(define-public r-amplican
+  (package
+    (name "r-amplican")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "amplican" version))
+              (sha256
+               (base32
+                "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"))))
+    (properties `((upstream-name . "amplican")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-clustercrit
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-ggthemes
+           r-gridextra
+           r-gtable
+           r-iranges
+           r-knitr
+           r-matrix
+           r-matrixstats
+           r-rcpp
+           r-rmarkdown
+           r-s4vectors
+           r-shortread
+           r-stringr
+           r-waffle))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/valenlab/amplican")
+    (synopsis "Automated analysis of CRISPR experiments")
+    (description
+     "The package performs alignment of the amplicon reads, normalizes gathered
+data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents
+the results in the form of aggregated reports.  Data and statistics can be broken
+down by experiments, barcodes, user defined groups, guides and amplicons allowing
+for quick identification of potential problems.")
+    (license license:gpl3)))
+
 (define-public r-amountain
   (package
     (name "r-amountain")
-- 
2.38.1

bug#59840: [PATCH 1/3] gnu: Add r-clustercrit.

[Ricardo Wurmus]

Thanks, I applied this series with minor changes.

-- 
Ricardo