gnu: emacs-svg-icon: Fix grammar.

[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4a2a796..c1454f2 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -619,6 +619,32 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
      "This package exposes an annotation database generated from Ensembl.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
+  (package
+    (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
+    (version "3.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
+                              version 'annotation))
+       (sha256
+        (base32
+         "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
+    (properties
+     `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
+    (synopsis "Annotation package for TxDb object(s)")
+    (description
+     "This package exposes an annotation databases generated from UCSC by
+exposing these as TxDb objects.")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
   (package
     (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
@@ -1087,7 +1113,7 @@ package @code{affy}.")
     (properties `((upstream-name . "gageData")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/gageData")
-    (synopsis "Auxillary data for gage package")
+    (synopsis "Auxiliary data for the gage package")
     (description
      "This is a supportive data package for the software package @code{gage}.
 However, the data supplied here are also useful for gene set or pathway
@@ -2705,14 +2731,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.0.14")
+    (version "3.0.15")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1siabhjd0w7bb6v2gfhsm9j7c7c86z8m6lfsyl8p84h0zhjs2vrw"))))
+         "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2919,14 +2945,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.24.1")
+    (version "3.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
+         "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2935,6 +2961,7 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
        ("r-dbi" ,r-dbi)
+       ("r-dplyr" ,r-dplyr)
        ("r-ensembldb" ,r-ensembldb)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
@@ -6908,14 +6935,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.4.2")
+    (version "2.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
+         "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -7740,7 +7767,7 @@ accessibility data.")
     (description
      "@code{r-circrnaprofiler} is a computational framework for a comprehensive
 in silico analysis of @dfn{circular RNA} (circRNAs).  This computational
-framework allows to combine and analyze circRNAs previously detected by
+framework allows combining and analyzing circRNAs previously detected by
 multiple publicly available annotation-based circRNA detection tools.  It
 covers different aspects of circRNAs analysis from differential expression
 analysis, evolutionary conservation, biogenesis to functional analysis.")
@@ -8374,14 +8401,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.8.3")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
+         "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -10523,12 +10550,12 @@ experiments, and visualize de influence of the involved factors.")
      "https://bioconductor.org/packages/msmsTests")
     (synopsis "Differential LC-MS/MS expression tests")
     (description
-     "This packages provides statistical tests for label-free LC-MS/MS data
+     "This package provides statistical tests for label-free LC-MS/MS data
 by spectral counts, to discover differentially expressed proteins between two
 biological conditions.  Three tests are available: Poisson GLM regression,
 quasi-likelihood GLM regression, and the negative binomial of the edgeR
-package.The three models admit blocking factors to control for nuissance
-variables.To assure a good level of reproducibility a post-test filter is
+package.  The three models admit blocking factors to control for nuisance
+variables.  To assure a good level of reproducibility a post-test filter is
 available, where we may set the minimum effect size considered biologicaly
 relevant, and the minimum expression of the most abundant condition.")
     (license license:gpl2)))
@@ -10802,14 +10829,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.34.0")
+    (version "1.34.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+         "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11064,7 +11091,7 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
     (description
      "This package implements functions for combinatorial and differential
 analysis of ChIP-seq data.  It includes uni- and multivariate peak-calling,
-export to genome browser viewable files, and functi ons for enrichment
+export to genome browser viewable files, and functions for enrichment
 analyses.")
     (license license:artistic2.0)))