Merge branch 'master' into core-updates

1 files changed, 268 insertions, 43 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9b0dad9d7..0fd97b691e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
+;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
@@ -5849,14 +5849,14 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.4-5")
+    (version "2.4-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya"))))
+         "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -6673,19 +6673,21 @@ also known as views, in a controlled vocabulary.")
 (define-public r-bookdown
   (package
   (name "r-bookdown")
-  (version "0.5")
+  (version "0.6")
   (source (origin
             (method url-fetch)
             (uri (cran-uri "bookdown" version))
             (sha256
              (base32
-              "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp"))))
+              "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc"))))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-htmltools" ,r-htmltools)
      ("r-knitr" ,r-knitr)
      ("r-rmarkdown" ,r-rmarkdown)
-     ("r-yaml" ,r-yaml)))
+     ("r-yaml" ,r-yaml)
+     ("r-xfun" ,r-xfun)
+     ("ghc-pandoc" ,ghc-pandoc)))
   (home-page "https://github.com/rstudio/bookdown")
   (synopsis "Authoring books and technical documents with R markdown")
   (description "This package provides output formats and utilities for
@@ -6965,13 +6967,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.2")
+    (version "3.20.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9"))))
+                "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6993,13 +6995,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.24.2")
+    (version "1.24.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j"))))
+                "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7031,13 +7033,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.4")
+    (version "3.34.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f"))))
+                "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7086,13 +7088,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.0")
+    (version "1.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a"))))
+                "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7164,13 +7166,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.34.1")
+    (version "2.34.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k"))))
+                "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7322,13 +7324,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf"))))
+                "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7386,13 +7388,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.38.2")
+    (version "1.38.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d"))))
+                "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7431,13 +7433,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.30.0")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs"))))
+                "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7657,13 +7659,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.10.0")
+    (version "1.11.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca"))))
+                "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8362,14 +8364,14 @@ in SNV base substitution data.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.61")
+    (version "1.62")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i"))))
+         "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8467,14 +8469,14 @@ factors bound at the specific regions.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.71.0")
+    (version "0.79.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+         "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8941,13 +8943,13 @@ number detection tools.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn"))))
+                "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9311,14 +9313,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.4.0")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r"))))
+         "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9391,13 +9393,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.1.0")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+                "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9434,8 +9436,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-fnn" ,r-fnn)
        ("r-fpc" ,r-fpc)
        ("r-gdata" ,r-gdata)
-       ("r-ggjoy" ,r-ggjoy)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
        ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
@@ -9452,6 +9454,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ranger" ,r-ranger)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
        ("r-rocr" ,r-rocr)
@@ -9661,14 +9664,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj"))))
+         "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9685,14 +9688,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.28.0")
+    (version "2.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk"))))
+         "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9806,14 +9809,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+         "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9975,14 +9978,14 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gprofiler
   (package
     (name "r-gprofiler")
-    (version "0.6.1")
+    (version "0.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gProfileR" version))
        (sha256
         (base32
-         "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p"))))
+         "08dsnja3g8qvqlgwhx9c9f8p8psn3qr5ddn84dhizkgglj30v2wj"))))
     (properties `((upstream-name . "gProfileR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10401,6 +10404,228 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define-public r-hdf5array
+  (package
+    (name "r-hdf5array")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HDF5Array" version))
+       (sha256
+        (base32
+         "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
+    (properties `((upstream-name . "HDF5Array")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/HDF5Array")
+    (synopsis "HDF5 back end for DelayedArray objects")
+    (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets.  It supports delayed operations and
+block processing.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
+               (("'%s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5.a %s/libhdf5.a'"))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5))
+                            "hdf5")
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 ;; szip is non-free software
+                 (("cp \\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
+                  "PKG_LIBS = ${HDF5_LIB}\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5))))
+    (home-page "https://bioconductor.org/packages/Rhdf5lib")
+    (synopsis "HDF5 library as an R package")
+    (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+    (license license:artistic2.0)))
+
+(define-public r-beachmat
+  (package
+    (name "r-beachmat")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beachmat" version))
+       (sha256
+        (base32
+         "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
+    (build-system r-build-system)
+    (inputs
+     `(("hdf5" ,hdf5)))
+    (propagated-inputs
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
+    (home-page "https://bioconductor.org/packages/beachmat")
+    (synopsis "Compiling Bioconductor to handle each matrix type")
+    (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+    (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+  (package
+    (name "r-singlecellexperiment")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleCellExperiment" version))
+       (sha256
+        (base32
+         "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
+    (properties
+     `((upstream-name . "SingleCellExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+    (synopsis "S4 classes for single cell data")
+    (description "This package defines an S4 class for storing data from
+single-cell experiments.  This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+    (license license:gpl3)))
+
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-rjson" ,r-rjson)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-shinydashboard" ,r-shinydashboard)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-tximport" ,r-tximport)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/davismcc/scater")
+    (synopsis "Single-cell analysis toolkit for gene expression data in R")
+    (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+    (license license:gpl2+)))
+
+(define-public r-scran
+  (package
+    (name "r-scran")
+    (version "1.6.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scran" version))
+       (sha256
+        (base32
+         "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-dt" ,r-dt)
+       ("r-dynamictreecut" ,r-dynamictreecut)
+       ("r-edger" ,r-edger)
+       ("r-fnn" ,r-fnn)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-igraph" ,r-igraph)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scater" ,r-scater)
+       ("r-shiny" ,r-shiny)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-statmod" ,r-statmod)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-viridis" ,r-viridis)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://bioconductor.org/packages/scran")
+    (synopsis "Methods for single-cell RNA-Seq data analysis")
+    (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data.  Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+    (license license:gpl3)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package