[bug#54991] gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.

[bug#54991] gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.

[MadalinIonel.Patrascu]

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[bug#54991] [PATCH 1/3] gnu: Add r-adductdata.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bec3496057..6e4ed31154 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1166,6 +1166,30 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-adductdata
+  (package
+    (name "r-adductdata")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductData" version
+                                     'experiment))
+              (sha256
+               (base32
+                "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj"))))
+    (properties `((upstream-name . "adductData")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationhub r-experimenthub))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductData")
+    (synopsis
+     "Data from untargeted mass spectrometry of modifications to Cys34")
+    (description
+     "This package contains data from untargeted @dfn{mass spectrometry} (MS)
+of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
+albumin} (HSA).")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")

base-commit: 0c89fe9e17dc9e628c73959289464ac5f146c7cd
-- 
2.34.0

[bug#54991] [PATCH 2/3] gnu: Add r-orgmassspecr.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-orgmassspecr): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bc95eee065..17396d130c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1068,6 +1068,28 @@ (define-public r-oenb
 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
     (license license:gpl2+)))
 
+(define-public r-orgmassspecr
+  (package
+    (name "r-orgmassspecr")
+    (version "0.5-3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "OrgMassSpecR" version))
+              (sha256
+               (base32
+                "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
+    (properties `((upstream-name . "OrgMassSpecR")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "http://OrgMassSpec.github.io/")
+    (synopsis "Organic or biological mass spectrometry data analysis")
+    (description
+     "This package @code{OrgMassSpecR} is an extension of the @code{R}
+statistical computing language.  It contains functions to assist with organic
+or biological mass spectrometry data analysis.  Mass spectral libraries are
+available as companion packages.")
+    (license license:bsd-2)))
+
 (define-public r-scales
   (package
     (name "r-scales")
-- 
2.34.0

[bug#54991] [PATCH 3/3] gnu: Add r-adductomicsr.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6e4ed31154..2cd4c89aa9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1605,6 +1605,50 @@ (define-public r-absseq
 ranking by fold-change and visualization.")
     (license license:gpl3+)))
 
+(define-public r-adductomicsr
+  (package
+    (name "r-adductomicsr")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductomicsR" version))
+              (sha256
+               (base32
+                "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl"))))
+    (properties `((upstream-name . "adductomicsR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-adductdata
+                             r-ade4
+                             r-annotationhub
+                             r-bootstrap
+                             r-data-table
+                             r-dosnow
+                             r-dplyr
+                             r-dt
+                             r-experimenthub
+                             r-fastcluster
+                             r-foreach
+                             r-fpc
+                             r-mzr
+                             r-orgmassspecr
+                             r-pastecs
+                             r-pracma
+                             r-rcppeigen
+                             r-reshape2
+                             r-rvest
+                             r-smoother
+                             r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductomicsR")
+    (synopsis "Processing of adductomic mass spectral datasets")
+    (description
+     "This package @code{adductomicsR} processes data generated by the
+@dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
+peptides from spectra that has been corrected for mass drift and retention time
+drift and quantifies level mass spectral peaks from @dfn{first stage of mass
+spectrometry} (MS1) data.")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.34.0

bug#54991: gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.

[Ricardo Wurmus]

Applied, thanks!

-- 
Ricardo