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-rw-r--r--gnu/packages/bioconductor.scm97
1 files changed, 97 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a78903becc..80cf28c954 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1166,6 +1166,28 @@ datasets which are derived from the Allen Brain Atlas:
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")
@@ -1877,6 +1899,81 @@ but which also provides utilities which may be useful for other platforms.")
;; GPLv3.
(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-agimicrorna
+ (package
+ (name "r-agimicrorna")
+ (version "2.46.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AgiMicroRna" version))
+ (sha256
+ (base32
+ "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
+ (properties `((upstream-name . "AgiMicroRna")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affy
+ r-affycoretools
+ r-biobase
+ r-limma
+ r-preprocesscore))
+ (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
+ (synopsis
+ "Processing and differential expression analysis of Agilent microRNA chips")
+ (description
+ "@code{AgiMicroRna} provides useful functionality for the processing,
+quality assessment and differential expression analysis of Agilent microRNA
+array data. The package uses a limma-like structure to generate the processed
+data in order to make statistical inferences about differential expression
+using the linear model features implemented in limma. Standard Bioconductor
+objects are used so that other packages could be used as well.")
+ (license license:gpl3)))
+
(define-public r-aneufinder
(package
(name "r-aneufinder")