Merge remote-tracking branch 'origin/master' into staging

1 files changed, 428 insertions, 0 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 33f66ce8be..f1af34844f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-homo-sapiens
+  (package
+    (name "r-homo-sapiens")
+    (version "1.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
+              (sha256
+               (base32
+                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
+    (properties
+     `((upstream-name . "Homo.sapiens")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-go-db" ,r-go-db)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
+    (synopsis "Annotation package for the Homo.sapiens object")
+    (description
+     "This package contains the Homo.sapiens object to access data from
+several related annotation packages.")
+    (license license:artistic2.0)))
+
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
@@ -9241,6 +9268,296 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-erma
+  (package
+    (name "r-erma")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "erma" version))
+       (sha256
+        (base32
+         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-iranges" ,r-iranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/erma")
+    (synopsis "Epigenomic road map adventures")
+    (description
+     "The epigenomics road map describes locations of epigenetic marks in DNA
+from a variety of cell types.  Of interest are locations of histone
+modifications, sites of DNA methylation, and regions of accessible chromatin.
+This package presents a selection of elements of the road map including
+metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
+by Ernst and Kellis.")
+    (license license:artistic2.0)))
+
+(define-public r-ggbio
+  (package
+    (name "r-ggbio")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ggbio" version))
+       (sha256
+        (base32
+         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/tengfei/ggbio/issues/117
+         ;; This fix will be included in the next release.
+         (add-after 'unpack 'fix-typo
+           (lambda _
+             (substitute* "R/GGbio-class.R"
+               (("fechable") "fetchable"))
+             #t)))))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggally" ,r-ggally)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-gtable" ,r-gtable)
+       ("r-hmisc" ,r-hmisc)
+       ("r-iranges" ,r-iranges)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "http://www.tengfei.name/ggbio/")
+    (synopsis "Visualization tools for genomic data")
+    (description
+     "The ggbio package extends and specializes the grammar of graphics for
+biological data.  The graphics are designed to answer common scientific
+questions, in particular those often asked of high throughput genomics data.
+All core Bioconductor data structures are supported, where appropriate.  The
+package supports detailed views of particular genomic regions, as well as
+genome-wide overviews.  Supported overviews include ideograms and grand linear
+views.  High-level plots include sequence fragment length, edge-linked
+interval to data view, mismatch pileup, and several splicing summaries.")
+    (license license:artistic2.0)))
+
+(define-public r-gqtlbase
+  (package
+    (name "r-gqtlbase")
+    (version "1.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gQTLBase" version))
+       (sha256
+        (base32
+         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
+    (properties `((upstream-name . "gQTLBase")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is an upstream bug.
+         (add-after 'unpack 'fix-imports
+           (lambda _
+             (substitute* "NAMESPACE"
+               ((".*maxffmode.*") "")
+               (("importFrom\\(ff,.*") "import(ff)\n"))
+             #t)))))
+    (propagated-inputs
+     `(("r-batchjobs" ,r-batchjobs)
+       ("r-bbmisc" ,r-bbmisc)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-bit" ,r-bit)
+       ("r-doparallel" ,r-doparallel)
+       ("r-ff" ,r-ff)
+       ("r-ffbase" ,r-ffbase)
+       ("r-foreach" ,r-foreach)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gQTLBase")
+    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+    (description
+     "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+    (license license:artistic2.0)))
+
+(define-public r-gqtlstats
+  (package
+    (name "r-gqtlstats")
+    (version "1.21.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gQTLstats" version))
+       (sha256
+        (base32
+         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
+    (properties `((upstream-name . "gQTLstats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-batchjobs" ,r-batchjobs)
+       ("r-bbmisc" ,r-bbmisc)
+       ("r-beeswarm" ,r-beeswarm)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-erma" ,r-erma)
+       ("r-ffbase" ,r-ffbase)
+       ("r-foreach" ,r-foreach)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gqtlbase" ,r-gqtlbase)
+       ("r-hardyweinberg" ,r-hardyweinberg)
+       ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-mgcv" ,r-mgcv)
+       ("r-plotly" ,r-plotly)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-snpstats" ,r-snpstats)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gQTLstats")
+    (synopsis "Computationally efficient analysis for eQTL and allied studies")
+    (description
+     "This package provides tools for the computationally efficient analysis
+of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
+The software in this package aims to support refinements and functional
+interpretation of members of a collection of association statistics on a
+family of feature/genome hypotheses.")
+    (license license:artistic2.0)))
+
+(define-public r-gviz
+  (package
+    (name "r-gviz")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Gviz" version))
+       (sha256
+        (base32
+         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+    (properties `((upstream-name . "Gviz")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-digest" ,r-digest)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Gviz")
+    (synopsis "Plotting data and annotation information along genomic coordinates")
+    (description
+     "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data.  Gviz uses the biomaRt and the
+rtracklayer packages to perform live annotation queries to Ensembl and UCSC
+and translates this to e.g. gene/transcript structures in viewports of the
+grid graphics package.  This results in genomic information plotted together
+with your data.")
+    (license license:artistic2.0)))
+
+(define-public r-gwascat
+  (package
+    (name "r-gwascat")
+    (version "2.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gwascat" version))
+       (sha256
+        (base32
+         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-readr" ,r-readr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gwascat")
+    (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
+    (description
+     "This package provides tools for representing and modeling data in the
+EMBL-EBI GWAS catalog.")
+    (license license:artistic2.0)))
+
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
@@ -9267,6 +9584,68 @@ maintaining all essential pathway attributes.  The package offers
 functionalities including parsing, graph operation, visualization and etc.")
     (license license:gpl2+)))
 
+(define-public r-ldblock
+  (package
+    (name "r-ldblock")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ldblock" version))
+       (sha256
+        (base32
+         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-httr" ,r-httr)
+       ("r-matrix" ,r-matrix)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/ldblock")
+    (synopsis "Data structures for linkage disequilibrium measures in populations")
+    (description
+     "This package defines data structures for @dfn{linkage
+disequilibrium} (LD) measures in populations.  Its purpose is to simplify
+handling of existing population-level data for the purpose of flexibly
+defining LD blocks.")
+    (license license:artistic2.0)))
+
+;; This is a CRAN package, but it depends on r-snpstats, which is a
+;; Bioconductor package.
+(define-public r-ldheatmap
+  (package
+    (name "r-ldheatmap")
+    (version "1.0-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "LDheatmap" version))
+       (sha256
+        (base32
+         "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
+    (properties `((upstream-name . "LDheatmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genetics" ,r-genetics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-snpstats" ,r-snpstats)))
+    (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
+    (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
+    (description
+     "This package provides tools to produce a graphical display, as a heat
+map, of measures of pairwise linkage disequilibria between SNPs.  Users may
+optionally include the physical locations or genetic map distances of each SNP
+on the plot.")
+    (license license:gpl3)))
+
 (define-public r-pathview
   (package
     (name "r-pathview")
@@ -9300,3 +9679,52 @@ graph with the mapped data.  In addition, @code{r-pathview} also seamlessly
 integrates with pathway and gene set (enrichment) analysis tools for
 large-scale and fully automated analysis.")
     (license license:gpl3+)))
+
+(define-public r-snpstats
+  (package
+    (name "r-snpstats")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "snpStats" version))
+       (sha256
+        (base32
+         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
+    (properties `((upstream-name . "snpStats")))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-matrix" ,r-matrix)
+       ("r-survival" ,r-survival)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/snpStats")
+    (synopsis "Methods for SNP association studies")
+    (description
+     "This package provides classes and statistical methods for large
+@dfn{single-nucleotide polymorphism} (SNP) association studies.  This extends
+the earlier snpMatrix package, allowing for uncertainty in genotypes.")
+    (license license:gpl3)))
+
+(define-public r-sushi
+  (package
+    (name "r-sushi")
+    (version "1.28.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Sushi" version))
+              (sha256
+               (base32
+                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
+    (properties `((upstream-name . "Sushi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biomart" ,r-biomart)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://bioconductor.org/packages/Sushi")
+    (synopsis "Tools for visualizing genomics data")
+    (description
+     "This package provides flexible, quantitative, and integrative genomic
+visualizations for publication-quality multi-panel figures.")
+    (license license:gpl2+)))