1 files changed, 61 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14daf59c92..4b9cd22f86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7100,6 +7100,41 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
+  (package
+    (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
+    (version "3.4.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "TxDb.Mmusculus.UCSC.mm10.knownGene_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+    (properties
+     `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-annotationdbi" ,r-annotationdbi)))
+    (home-page
+     "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
+    (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
+    (description
+     "This package loads a TxDb object, which is an R interface to
+prefabricated databases contained in this package.  This package provides
+the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
+based on the knownGene track.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")
@@ -7960,3 +7995,29 @@ immunoprecipitation and target enrichment on small gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
     (license license:gpl2)))
+
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genefilter" ,r-genefilter)))
+    (home-page "http://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment.  It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets.  Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))