Merge remote-tracking branch 'origin/master' into core-updates-frozen

1 files changed, 269 insertions, 15 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5d29a3acf2..a25f56ad02 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
+;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -286,6 +287,28 @@ RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
 Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-drerio-ucsc-danrer11
+  (package
+    (name "r-bsgenome-drerio-ucsc-danrer11")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
+                              version 'annotation))
+       (sha256
+        (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
+    (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)))
+    (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
+    (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
+    (description
+     "This package provides full genome sequences for Danio rerio (Zebrafish)
+as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
   (package
     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
@@ -1588,6 +1611,33 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 @code{Matrix} objects, and ordinary arrays and data frames.")
     (license license:artistic2.0)))
 
+(define-public r-derfinderhelper
+  (package
+    (name "r-derfinderhelper")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "derfinderHelper" version))
+       (sha256
+        (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"))))
+    (properties `((upstream-name . "derfinderHelper")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/leekgroup/derfinderHelper")
+    (synopsis "Helper for derfinder")
+    (description
+     "This package speeds up the derfinder package when using multiple cores.
+It is particularly useful when using BiocParallel and it helps reduce the time
+spent loading the full derfinder package when running the F-statistics
+calculation in parallel.")
+    (license license:artistic2.0)))
+
 (define-public r-bluster
   (package
    (name "r-bluster")
@@ -2234,13 +2284,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.50.0")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "069wqihm8pj3r41dizvdbj4jnw9bsc5jrz8czfrak5v69bgk5v5q"))))
+                "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -2272,13 +2322,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.28.0")
+    (version "1.28.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0jqgbpjppwinzw100qhc42kc95znq6xanl26bi8m9cq7yggbpra6"))))
+                "04s6y7q9dvg26fazs6lzkm668zpl3136j9gd5hkyihyrf4a1w3g3"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -3164,13 +3214,13 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.46.0")
+    (version "1.46.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "03fdmzcf8h17ksa3byc3k5mxc65pqrbcnw00myz1q53l01p3cnf2"))))
+                "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -4143,6 +4193,46 @@ differential expression analysis, RNAseq data and related problems.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
+(define-public r-scdblfinder
+  (package
+    (name "r-scdblfinder")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scDblFinder" version))
+       (sha256
+        (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd"))))
+    (properties `((upstream-name . "scDblFinder")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-bluster" ,r-bluster)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-igraph" ,r-igraph)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scater" ,r-scater)
+       ("r-scran" ,r-scran)
+       ("r-scuttle" ,r-scuttle)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-xgboost" ,r-xgboost)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/plger/scDblFinder")
+    (synopsis "Detect multiplets in single-cell RNA sequencing data")
+    (description
+     "The scDblFinder package gathers various methods for the detection and
+handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
+multiple cells captured within the same droplet or reaction volume).  It
+includes methods formerly found in the scran package, and the new fast and
+comprehensive scDblFinder method.")
+    (license license:gpl3)))
+
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
@@ -4337,6 +4427,39 @@ events and allows for the incorporation of prior knowledge through supervised
 graph construction.")
    (license license:artistic2.0)))
 
+(define-public r-stringdb
+  (package
+    (name "r-stringdb")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "STRINGdb" version))
+       (sha256
+        (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"))))
+    (properties `((upstream-name . "STRINGdb")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gplots" ,r-gplots)
+       ("r-hash" ,r-hash)
+       ("r-igraph" ,r-igraph)
+       ("r-plotrix" ,r-plotrix)
+       ("r-plyr" ,r-plyr)
+       ("r-png" ,r-png)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcurl" ,r-rcurl)
+       ("r-sqldf" ,r-sqldf)))
+    (home-page "https://git.bioconductor.org/packages/STRINGdb")
+    (synopsis "Search tool for the retrieval of interacting proteins database")
+    (description
+     "The @code{STRINGdb} package provides an R interface to the STRING
+protein-protein interactions database.  @url{https://www.string-db.org,
+STRING} is a database of known and predicted protein-protein interactions.
+The interactions include direct (physical) and indirect (functional)
+associations.  Each interaction is associated with a combined confidence score
+that integrates the various evidences.")
+    (license license:gpl2)))
+
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
@@ -4613,6 +4736,69 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+(define-public r-xina
+  (package
+    (name "r-xina")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "XINA" version))
+       (sha256
+        (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"))))
+    (properties `((upstream-name . "XINA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-alluvial" ,r-alluvial)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-igraph" ,r-igraph)
+       ("r-mclust" ,r-mclust)
+       ("r-plyr" ,r-plyr)
+       ("r-stringdb" ,r-stringdb)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://git.bioconductor.org/packages/XINA")
+    (synopsis "Identifying proteins that exhibit similar patterns")
+    (description
+     "The aim of @code{XINA} is to determine which proteins exhibit similar
+patterns within and across experimental conditions, since proteins with
+co-abundance patterns may have common molecular functions.  @code{XINA} imports
+multiple datasets, tags dataset in silico, and combines the data for subsequent
+subgrouping into multiple clusters.  The result is a single output depicting
+the variation across all conditions.  @code{XINA} not only extracts
+coabundance profiles within and across experiments, but also incorporates
+protein-protein interaction databases and integrative resources such as
+@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
+molecular functions, respectively, and produces intuitive graphical outputs.")
+    (license license:gpl3)))
+
+(define-public r-xmapbridge
+  (package
+    (name "r-xmapbridge")
+    (version "1.52.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "xmapbridge" version))
+       (sha256
+        (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi"))))
+    (properties `((upstream-name . "xmapbridge")))
+    (build-system r-build-system)
+    (home-page "https://git.bioconductor.org/packages/xmapbridge")
+    (synopsis "Display numeric data in the web based genome browser X:MAP")
+    (description
+     "The package @code{xmapbridge} can plot graphs in the X:Map genome
+browser.  X:Map uses the Google Maps API to provide a scrollable view of the
+genome.  It supports a number of species, and can be accessed at
+@url{http://xmap.picr.man.ac.uk}.  This package exports plotting files in a
+suitable format.  Graph plotting in R is done using calls to the functions
+@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
+similar to those used by the standard plot methods in R.  These result in data
+being written to a set of files (in a specific directory structure) that
+contain the data to be displayed, as well as some additional meta-data
+describing each of the graphs.")
+    (license license:lgpl3)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
@@ -7420,14 +7606,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.20.0")
+    (version "3.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "0hj5hn54g8a3gj4q9200bffcy9m1mvkiwbg60ysv1hxxbpi57kmv"))))
+         "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8791,14 +8977,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.16.0")
+    (version "3.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "0m6w68ndf2a4k148pbb0bbbgq57akzqgi9nf7k6ngkk22j3m7m95"))))
+         "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -9837,7 +10023,6 @@ statistics to the plot.")
        ("r-flowviz" ,r-flowviz)
        ("r-graph" ,r-graph)
        ("r-mnormt" ,r-mnormt)))
-    #;
     (inputs
      `(("gsl" ,gsl)))
     (native-inputs
@@ -10114,14 +10299,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.18.0")
+    (version "6.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0jwkb5scc33nfn2mibga8vp00pmc24ham71gpkbizvy43cy85icf"))))
+         "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11523,6 +11708,37 @@ visualization functions for compound clustering results and chemical
 structures.")
     (license license:artistic2.0)))
 
+(define-public r-fmcsr
+  (package
+    (name "r-fmcsr")
+    (version "1.36.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "fmcsR" version))
+        (sha256
+          (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0"))))
+    (properties `((upstream-name . "fmcsR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-chemminer" ,r-chemminer)
+       ("r-runit" ,r-runit)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/girke-lab/fmcsR")
+    (synopsis "Mismatch tolerant maximum common substructure searching")
+    (description
+     "The fmcsR package introduces an efficient @dfn{maximum common
+substructure} (MCS) algorithms combined with a novel matching strategy that
+allows for atom and/or bond mismatches in the substructures shared among two
+small molecules.  The resulting flexible MCSs (FMCSs) are often larger than
+strict MCSs, resulting in the identification of more common features in their
+source structures, as well as a higher sensitivity in finding compounds with
+weak structural similarities.  The fmcsR package provides several utilities to
+use the FMCS algorithm for pairwise compound comparisons, structure similarity
+searching and clustering.")
+    (license license:artistic2.0)))
+
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
@@ -12379,13 +12595,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.32.2")
+    (version "0.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0xrmii2dnwyknpjdiwwjlklgzpbk9q09br27rq5ffz08if9yyk20"))))
+                "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -14882,3 +15098,41 @@ and other associated metadata.  De novo transcriptomes can be linked to the
 appropriate sources with linkedTxomes and shared for computational
 reproducibility.")
     (license license:gpl2)))
+
+(define-public r-phyloseq
+  (package
+    (name "r-phyloseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "phyloseq" version))
+       (sha256
+        (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"))))
+    (properties `((upstream-name . "phyloseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ade4" ,r-ade4)
+       ("r-ape" ,r-ape)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomformat" ,r-biomformat)
+       ("r-biostrings" ,r-biostrings)
+       ("r-cluster" ,r-cluster)
+       ("r-data-table" ,r-data-table)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-igraph" ,r-igraph)
+       ("r-multtest" ,r-multtest)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-scales" ,r-scales)
+       ("r-vegan" ,r-vegan)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/joey711/phyloseq")
+    (synopsis "Handling and analysis of high-throughput microbiome census data")
+    (description
+     "Phyloseq provides a set of classes and tools to facilitate the import,
+storage, analysis, and graphical display of microbiome census data.")
+    (license license:agpl3)))