[bug#66843] [PATCH] gnu: Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

[bug#66843] [PATCH] gnu: Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-radiogx, r-coregx, r-piano, r-r4rna 
and r-r3cseq): New variables.

* gnu/packages/cran.scm (r-bench, r-profmem, r-relations, r-magicaxis, 
r-celestial, r-nistunits): New variables.

[bug#66843] [PATCH 01/11] gnu: Add r-r3cseq.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-r3cseq): New variable.

Change-Id: Ib62db1415ef3988ccef88ad600192246964b4d84
---
 gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3ff0b1127..dee72de2b7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7747,6 +7747,38 @@ (define-public r-hpar
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-r3cseq
+  (package
+    (name "r-r3cseq")
+    (version "1.46.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "r3Cseq" version))
+       (sha256
+        (base32 "1wpjsiy9qh45h3k5s79w4zhkma5h4gvyf2sa8l934mx0jl16k0q2"))))
+    (properties `((upstream-name . "r3Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-data-table
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-qvalue
+           r-rcolorbrewer
+           r-rsamtools
+           r-rtracklayer
+           r-sqldf
+           r-vgam))
+    (home-page "http://r3cseq.genereg.net/Site/index.html")
+    (synopsis
+     "Analysis of Chromosome conformation capture and Next-generation sequencing")
+    (description
+     "This package is used for the analysis of long-range chromatin interactions from
+3C-seq assay.")
+    (license license:gpl3)))
+
 (define-public r-raggedexperiment
   (package
     (name "r-raggedexperiment")

base-commit: d22d2a05c389207f8cdcf824be7738b1499a987c
-- 
2.41.0

[bug#66843] [PATCH 02/11] gnu: Add r-r4rna.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-r4rna): New variable.

Change-Id: I1bde2a17b0ba4a97fa54161744f048dbfaf2217a
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dee72de2b7..6a3606b399 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7779,6 +7779,29 @@ (define-public r-r3cseq
 3C-seq assay.")
     (license license:gpl3)))
 
+(define-public r-r4rna
+  (package
+    (name "r-r4rna")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "R4RNA" version))
+       (sha256
+        (base32 "1i4c9477xsp3hq5kxydrimhl6g8vshwbqgnhap5n1ykxbsval1pp"))))
+    (properties `((upstream-name . "R4RNA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biostrings))
+    (home-page "https://www.e-rna.org/r-chie/")
+    (synopsis "RNA visualization and analysis")
+    (description
+     "This package provides a package for RNA basepair analysis, including the
+visualization of basepairs as arc diagrams for easy comparison and annotation of
+sequence and structure.  Arc diagrams can additionally be projected onto
+multiple sequence alignments to assess basepair conservation and covariation,
+with numerical methods for computing statistics for each.")
+    (license license:gpl3)))
+
 (define-public r-raggedexperiment
   (package
     (name "r-raggedexperiment")
-- 
2.41.0

[bug#66843] [PATCH 03/11] gnu: Add r-nistunits.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-nistunits): New variable.

Change-Id: I66328b54045a3125e5f3033605be88e3a1b2646a
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de31f44dbd..fe8014c381 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9817,6 +9817,27 @@ (define-public r-network
 supports arbitrary vertex/edge/graph attributes.")
     (license license:gpl2+)))
 
+(define-public r-nistunits
+  (package
+    (name "r-nistunits")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NISTunits" version))
+       (sha256
+        (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a"))))
+    (properties `((upstream-name . "NISTunits")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=NISTunits")
+    (synopsis "Fundamental physical constants and unit conversions")
+    (description
+     "Fundamental physical constants (quantity, value, uncertainty, unit) for
+@acronym{SI, International System of Units} and non-SI units, plus unit
+conversions based on the data from @acronym{NIST, National Institute of
+Standards and Technology}, USA.")
+    (license license:gpl3+)))
+
 (define-public r-stabs
   (package
     (name "r-stabs")
-- 
2.41.0

[bug#66843] [PATCH 04/11] gnu: Add r-celestial.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-celestial): New variable.

Change-Id: I9ab9c6b6c79f2fb12d7391a75e7214bbeba675fc
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fe8014c381..cc3ac02599 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -305,6 +305,30 @@ (define-public r-changepoint
     ;; Any version of the GPL.
     (license license:gpl3+)))
 
+(define-public r-celestial
+  (package
+    (name "r-celestial")
+    (version "1.4.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "celestial" version))
+       (sha256
+        (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z"))))
+    (properties `((upstream-name . "celestial")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-nistunits r-pracma r-rann))
+    (home-page "https://cran.r-project.org/package=celestial")
+    (synopsis
+     "Collection of common astronomical conversion routines and functions")
+    (description
+     "This package contains a number of common astronomy conversion routines,
+particularly the HMS and degrees schemes, which can be fiddly to convert between
+on mass due to the textural nature of the former.  It allows users to coordinate
+match datasets quickly.  It also contains functions for various cosmological
+calculations.")
+    (license license:gpl3)))
+
 ;; The package sources include multiple non-minified JavaScript files and the
 ;; v5.1.0 variant of d3.js.  The d3.js file is not minified.
 (define-public r-chromomap
-- 
2.41.0

[bug#66843] [PATCH 05/11] gnu: Add r-magicaxis.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-magicaxis): New variable.

Change-Id: I9843dcf90cd6d85799fab688d6dccfcfacfad672
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cc3ac02599..b4770f8a53 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7777,6 +7777,33 @@ (define-public r-magic
 dimensioned arrays.")
     (license license:gpl2)))
 
+(define-public r-magicaxis
+  (package
+    (name "r-magicaxis")
+    (version "2.2.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "magicaxis" version))
+       (sha256
+        (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v"))))
+    (properties `((upstream-name . "magicaxis")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-celestial
+           r-mapproj
+           r-mass
+           r-plotrix
+           r-rann
+           r-sm))
+    (home-page "https://cran.r-project.org/package=magicaxis")
+    (synopsis "Scientific plotting with minor-tick and log minor-tick support")
+    (description
+     "This package provides functions to make useful (and pretty) plots for
+scientific plotting.  Additional plotting features are added for base plotting,
+with particular emphasis on making attractive log axis plots.")
+    (license license:gpl3)))
+
 (define-public r-rmysql
   (package
     (name "r-rmysql")
-- 
2.41.0

[bug#66843] [PATCH 06/11] gnu: Add r-relations.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-relations): New variable.

Change-Id: I4bf67353aa7f7221592d274d61c74b83191a6281
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b4770f8a53..ef43771f47 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3456,6 +3456,27 @@ (define-public r-selectr
 package is a port of the Python package @code{cssselect}.")
     (license license:bsd-3)))
 
+(define-public r-relations
+  (package
+    (name "r-relations")
+    (version "0.6-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "relations" version))
+       (sha256
+        (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq"))))
+    (properties `((upstream-name . "relations")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-cluster r-sets r-slam))
+    (home-page "https://cran.r-project.org/package=relations")
+    (synopsis "Data structures and algorithms for relations")
+    (description
+     "This package provides data structures and algorithms for k-ary relations
+with arbitrary domains, featuring relational algebra, predicate functions, and
+fitters for consensus relations.")
+    (license license:gpl2)))
+
 (define-public r-repmis
   (package
     (name "r-repmis")
-- 
2.41.0

[bug#66843] [PATCH 07/11] gnu: Add r-profmem.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-profmem): New variable.

Change-Id: If99cf8e963601e9f0a664f12ef263a064b59b0d6
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ef43771f47..27ea2cdc06 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1266,6 +1266,38 @@ (define-public r-prettydoc
 highlight styles are supported.")
     (license license:asl2.0)))
 
+(define-public r-profmem
+  (package
+    (name "r-profmem")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "profmem" version))
+       (sha256
+        (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l"))))
+    (properties `((upstream-name . "profmem")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list r-r-rsp
+           r-markdown)) ; for vignettes
+    (home-page "https://github.com/HenrikBengtsson/profmem")
+    (synopsis "Simple memory profiling for R")
+    (description
+     "This package provides a simple and light-weight API for memory profiling
+of R expressions.  The profiling is built on top of R's built-in memory profiler
+@code{utils::Rprofmem()}, which records every memory allocation done by R (also
+native code).")
+    (license license:lgpl2.1+)))
+
 (define-public r-proj4
   (package
     (name "r-proj4")
-- 
2.41.0

[bug#66843] [PATCH 08/11] gnu: Add r-bench.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-bench): New variable.

Change-Id: I9948ff12729b08dd4016df272777651a6b6de2e0
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 27ea2cdc06..af9b59c8bf 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1481,6 +1481,26 @@ (define-public r-babelwhale
 volume or copy a file.")
     (license license:expat)))
 
+(define-public r-bench
+  (package
+    (name "r-bench")
+    (version "1.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bench" version))
+       (sha256
+        (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz"))))
+    (properties `((upstream-name . "bench")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble))
+    (home-page "https://bench.r-lib.org/")
+    (synopsis "High precision timing of R expressions")
+    (description
+     "This package provides tools to accurately benchmark and analyze execution
+times for R expressions.")
+    (license license:expat)))
+
 (define-public r-benchmarkmedata
   (package
     (name "r-benchmarkmedata")
-- 
2.41.0

[bug#66843] [PATCH 09/11] gnu: Add r-piano.

[Mădălin Ionel Patrașcu]

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

Change-Id: I1bc2387563510c47614748423a3b510adc0486aa
---
 gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6a3606b399..e2fd9c5016 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9109,6 +9109,43 @@ (define-public r-pfamanalyzer
 domain isotypes from pfam data.")
     (license license:expat)))
 
+(define-public r-piano
+  (package
+    (name "r-piano")
+    (version "2.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "piano" version))
+       (sha256
+        (base32 "0rm9afgq4n7yinmx09b0xd17wgzhbswm80vcjmmwxr6fv1741xfy"))))
+    (properties `((upstream-name . "piano")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dt
+           r-fgsea
+           r-gplots
+           r-htmlwidgets
+           r-igraph
+           r-marray
+           r-relations
+           r-scales
+           r-shiny
+           r-shinydashboard
+           r-shinyjs
+           r-visnetwork))
+    (native-inputs (list r-knitr))
+    (home-page "https://varemo.github.io/piano/")
+    (synopsis "Platform for integrative analysis of omics data")
+    (description
+     "Piano performs gene set analysis using various statistical methods, from
+different gene level statistics and a wide range of gene-set collections.  The
+package contains functions for combining the results of multiple runs of gene
+set analyses.")
+    (license license:gpl2+)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package:
 ;; r-aroma-light, r-dnacopy..
 (define-public r-pscbs
-- 
2.41.0

[bug#66843] [PATCH 10/11] gnu: Add r-coregx.

[Mădălin Ionel Patrașcu]

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

Change-Id: Ib54ba3c7bebdcc90748d4e4b0b2ce63b7f0fc1b8
---
 gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e2fd9c5016..091cf98b5c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4422,6 +4422,52 @@ (define-public r-cellid
 enrichment in single cell data.")
     (license license:gpl3)))
 
+(define-public r-coregx
+  (package
+    (name "r-coregx")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CoreGx" version))
+       (sha256
+        (base32 "09pv117g8sxhrij960mparrz1r9vx8s20gmpvn1h667kl1bc0jm9"))))
+    (properties `((upstream-name . "CoreGx")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bench
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-bumpymatrix
+           r-checkmate
+           r-crayon
+           r-data-table
+           r-glue
+           r-lsa
+           r-matrixgenerics
+           r-multiassayexperiment
+           r-piano
+           r-rlang
+           r-s4vectors
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/CoreGx")
+    (synopsis
+     "Classes and functions to serve as the basis for other Gx packages")
+    (description
+     "This package provides a collection of functions and classes which serve as
+the foundation for our lab's suite of R packages, such as PharmacoGx and RadioGx.
+It was created to abstract shared functionality from other lab package releases
+to increase ease of maintainability and reduce code repetition in current and
+future Gx suite programs.  Major features include a @code{CoreSet} class, from
+which RadioSet and PharmacoSet are derived, along with get and set methods for
+each respective slot.  Additional functions related to fitting and plotting dose
+response curves, quantifying statistical correlation and calculating
+@acronym{AUC, area under the curve} or @acronym{SF, survival fraction} are
+included.")
+    (license license:gpl3+)))
+
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-- 
2.41.0

[bug#66843] [PATCH 11/11] gnu: Add r-radiogx.

[Mădălin Ionel Patrașcu]

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

Change-Id: I8fd06a18bd68f9a3baa2cc129d62aef06528bc97
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 091cf98b5c..69adea13e5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7848,6 +7848,50 @@ (define-public r-r4rna
 with numerical methods for computing statistics for each.")
     (license license:gpl3)))
 
+(define-public r-radiogx
+  (package
+    (name "r-radiogx")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RadioGx" version))
+       (sha256
+        (base32 "18zqfnwjil4mv7fgh4wvnniyybmyqkg0hk2wc57rcn0mlppa3602"))))
+    (properties `((upstream-name . "RadioGx")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-catools
+           r-coregx
+           r-data-table
+           r-downloader
+           r-magicaxis
+           r-matrixstats
+           r-rcolorbrewer
+           r-reshape2
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/RadioGx")
+    (synopsis "Analysis of large-scale radio-genomic data")
+    (description
+     "This package is a computational tool box for radio-genomic analysis which
+integrates radio-response data, radio-biological modelling and comprehensive
+cell line annotations for hundreds of cancer cell lines.  The @code{RadioSet}
+class enables creation and manipulation of standardized datasets including
+information about cancer cells lines, radio-response assays and dose-response
+indicators.  Included methods allow fitting and plotting dose-response data
+using established radio-biological models along with quality control to validate
+results.  Additional functions related to fitting and plotting dose response
+curves, quantifying statistical correlation and calculating @acronym{AUC, area
+under the curve} or @acronym{SF, survival fraction} are included.")
+    (license license:gpl3)))
+
 (define-public r-raggedexperiment
   (package
     (name "r-raggedexperiment")
-- 
2.41.0

bug#66843: [PATCH] gnu: Add r-radiogx, r-coregx, r-piano, r-bench, r-profmem, r-relations, r-magicaxis, r-celestial, r-nistunits, r-r4rna and r-r3cseq.

[Ricardo Wurmus]

I’ve applied them all with some changes to the descriptions.

-- 
Ricardo