[bug#62297] [PATCH] gnu: Add r-affyilm, r-affyplm, r-affylmgui, r-annotationhubdata and r-tkrplot.

[bug#62297] [PATCH] gnu: Add r-affyilm, r-affyplm, r-affylmgui, r-annotationhubdata and r-tkrplot.

[MadalinIonel.Patrascu]

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* gnu/packages/bioconductor.scm (r-affyilm, r-affyplm, r-affylmgui, r-annotationhubdata): New variables.
* gnu/packages/cran.scm (r-tkrplot): New variable.

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[bug#62297] [PATCH 1/5] gnu: Add r-affyilm.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-affyilm): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e54c9ccf2b..48aa426574 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2098,6 +2098,32 @@ (define-public r-affixcan
 expression values are known.")
     (license license:gpl3)))
 
+(define-public r-affyilm
+  (package
+    (name "r-affyilm")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyILM" version))
+       (sha256
+        (base32 "0i2hjaqjz06ym5kbw5da1h3cahc630mjwljsji1l2ks0gjcipll0"))))
+    (properties `((upstream-name . "affyILM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affxparser
+           r-affy
+           r-biobase
+           r-gcrma))
+    (home-page "https://bioconductor.org/packages/affyILM")
+    (synopsis "Linear model of background subtraction and the Langmuir isotherm")
+    (description
+     "The affyILM package is a preprocessing tool which estimates gene expression
+levels for Affymetrix Gene Chips.  Input from physical chemistry is employed to
+first background subtract intensities before calculating concentrations on behal
+of the Langmuir model.")
+    (license license:gpl3)))
+
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")

base-commit: 1f36534c7e8f2325bff4df5d37ecc811dc63fc38
-- 
2.39.2

[bug#62297] [PATCH 2/5] gnu: Add r-affyplm.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-affyplm): New variable.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 48aa426574..1e3753b2ec 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2124,6 +2124,36 @@ (define-public r-affyilm
 of the Langmuir model.")
     (license license:gpl3)))
 
+(define-public r-affyplm
+  (package
+    (name "r-affyplm")
+    (version "1.74.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyPLM" version))
+       (sha256
+        (base32 "0f0faxjzlg0znhjfvf1490yc54npkx659jx76cddm5hk7q0blv3v"))))
+    (properties `((upstream-name . "affyPLM")))
+    (build-system r-build-system)
+     (inputs (list zlib))
+    (propagated-inputs
+     (list r-affy
+           r-biobase
+           r-biocgenerics
+           r-gcrma
+           r-preprocesscore
+           r-zlibbioc))
+    (home-page "https://github.com/bmbolstad/affyPLM")
+    (synopsis "Methods for fitting probe-level models")
+    (description
+     "The affyPLM provides a package that extends and improves the functionality
+of the base affy package.  For speeding up the runs, it includes routines that make
+heavy use of compiled code.  The central focus is on implementation of methods for
+fitting probe-level models and tools using these models.  @acronym{PLM, Product
+Lifecycle Management} based quality assessment tools are also provided.")
+    (license license:gpl2+)))
+
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
-- 
2.39.2

[bug#62297] [PATCH 3/5] gnu: Add r-tkrplot.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-tkrplot): 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 39e692fc6c..909943fdcc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2818,6 +2818,30 @@ (define-public r-tidyverse
 single step.")
     (license license:gpl3)))
 
+(define-public r-tkrplot
+  (package
+    (name "r-tkrplot")
+    (version "0.0-27")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tkrplot" version))
+       (sha256
+        (base32 "19bj4wn1fs4wrx5k4gakhpz4q59fgx0584wyaw7hnh0ljj8i34n9"))))
+    (properties `((upstream-name . "tkrplot")))
+    (build-system r-build-system)
+    (inputs (list libx11))
+    (home-page "https://cran.r-project.org/package=tkrplot")
+    (synopsis "Simple mechanism for placing R graphics in a Tk widget")
+    (description
+     "The tkrplot package creates and returns a @dfn{Tk, cross-platform graphical
+user interface toolkit} label widget containing a Tk image of type Rplot.  The plot
+is created by calling fun with a special device used create the image.  The function
+@code{tkrreplot} calls fun to place a new plot in the Rplot widget lab.  @code{
+tkpersp} is called like @code{persp} but produces a plot in which some of the
+parameters of persp are controlled graphically.")
+    (license (list license:gpl2+ license:gpl3+)))) ;; expanded from GPL
+
 (define-public r-rvest
   (package
     (name "r-rvest")
-- 
2.39.2

[bug#62297] [PATCH 4/5] gnu: Add r-affylmgui.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-affylmgui): New variable.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e3753b2ec..78ce740c2c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2124,6 +2124,37 @@ (define-public r-affyilm
 of the Langmuir model.")
     (license license:gpl3)))
 
+(define-public r-affylmgui
+  (package
+    (name "r-affylmgui")
+    (version "1.72.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affylmGUI" version))
+       (sha256
+        (base32 "0jds73pxqf522wcg8qd4b4k1qbhn51av5md1nhgcdnb6is0lzvxi"))))
+    (properties `((upstream-name . "affylmGUI")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-affyio
+           r-affyplm
+           r-annotationdbi
+           r-biocgenerics
+           r-biocmanager
+           r-gcrma
+           r-limma
+           r-r2html
+           r-tkrplot
+           r-xtable))
+    (home-page "http://bioinf.wehi.edu.au/affylmGUI/")
+    (synopsis "GUI for limma package with Affymetrix microarrays")
+    (description
+     "This package provides a @acronym{GUI, Graphical User Interface} for analysis
+of Affymetrix microarray gene expression data using the affy and limma packages.")
+    (license license:gpl2+)))
+
 (define-public r-affyplm
   (package
     (name "r-affyplm")
-- 
2.39.2

[bug#62297] [PATCH 5/5] gnu: Add r-annotationhubdata.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-annotationhubdata): New variable.
---
 gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 78ce740c2c..8ebdcc3706 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2704,6 +2704,59 @@ (define-public r-animalcules
 to understand their data better and discover new insights.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhubdata
+  (package
+    (name "r-annotationhubdata")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHubData" version))
+       (sha256
+        (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"))))
+    (properties `((upstream-name . "AnnotationHubData")))
+    (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"))))))
+    (propagated-inputs
+     (list r-annotationdbi
+           r-annotationforge
+           r-annotationhub
+           r-biobase
+           r-bioccheck
+           r-biocgenerics
+           r-biocmanager
+           r-biocviews
+           r-biostrings
+           r-dbi
+           r-futile-logger
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-jsonlite
+           r-organismdbi
+           r-rcurl
+           r-rsamtools
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AnnotationHubData")
+    (synopsis "Transform public data resources into Bioconductor data structures")
+    (description
+     "These recipes convert a wide variety and a growing number of public bioinformatic
+data sets into easily-used standard Bioconductor data structures.")
+    (license license:artistic2.0)))
+
 (define-public r-anvil
   (package
     (name "r-anvil")
-- 
2.39.2

bug#62297: [PATCH 1/5] gnu: Add r-affyilm.

[Ricardo Wurmus]

Thanks for the patches.  I edited the formatting (M-q in Emacs) and
edited some of the descriptions.

Applied!

-- 
Ricardo