gnu: spice-gtk: Add an absolute reference for libjpeg in the .la files.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c7892f8..2fbfdba 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1958,14 +1958,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.20.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
+         "0mqb899wah5n7bp2lajhwy2zpqqhi18plza3i3m51rfl9n62smph"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -1986,6 +1986,8 @@ experiments.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-stringr" ,r-stringr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
     (synopsis "R package for handling genomic interaction data")
     (description
@@ -2649,6 +2651,8 @@ interactive exploration of results.")
        ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-stringr" ,r-stringr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/RGLab/MAST/")
     (synopsis "Model-based analysis of single cell transcriptomics")
     (description
@@ -3393,20 +3397,22 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.12.0")
+    (version "2.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya"))))
+         "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-go-db" ,r-go-db)
        ("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://guangchuangyu.github.io/software/GOSemSim")
     (synopsis "GO-terms semantic similarity measures")
     (description
@@ -4073,14 +4079,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35"))))
+         "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4091,6 +4097,8 @@ footprints.")
        ("r-mapplots" ,r-mapplots)
        ("r-rcpp" ,r-rcpp)
        ("r-vioplot" ,r-vioplot)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/GOfuncR/")
     (synopsis "Gene ontology enrichment using FUNC")
     (description
@@ -5316,14 +5324,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.14.0")
+    (version "1.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j"))))
+         "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -5332,10 +5340,7 @@ coefficients).")
        ("r-randomforest" ,r-randomforest)
        ("r-ropls" ,r-ropls)))
     (native-inputs
-     `(("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("pandoc" ,ghc-pandoc)
-       ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/biosigner/")
     (synopsis "Signature discovery from omics data")
     (description
@@ -5570,14 +5575,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8"))))
+         "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5591,6 +5596,8 @@ manipulation of flow cytometry data.")
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/RGLab/ggcyto/issues")
     (synopsis "Visualize Cytometry data with ggplot")
     (description
@@ -5826,14 +5833,14 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1"))))
+         "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
@@ -5863,6 +5870,8 @@ sequential way to mimic the manual gating strategy.")
        ("r-runit" ,r-runit)
        ("r-xml" ,r-xml)
        ("r-yaml" ,r-yaml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/RGLab/CytoML")
     (synopsis "GatingML interface for cross platform cytometry data sharing")
     (description
@@ -5903,14 +5912,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.10.8")
+    (version "6.10.9")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
+         "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5927,6 +5936,8 @@ self-organizing map clustering and minimal spanning trees.")
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-reshape2" ,r-reshape2)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "http://www.mixOmics.org")
     (synopsis "Multivariate methods for exploration of biological datasets")
     (description
@@ -6025,14 +6036,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.4.2")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r"))))
+         "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -6056,6 +6067,8 @@ genes in the gene-set that are ranked above the leading edge).")
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
        ("r-vgam" ,r-vgam)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/cicero/")
     (synopsis "Predict cis-co-accessibility from single-cell data")
     (description
@@ -6626,7 +6639,8 @@ measures.")
        ("r-gplots" ,r-gplots)
        ("r-limma" ,r-limma)
        ("r-rcolorbrewer" ,r-rcolorbrewer)))
-    (home-page "http://www.ebi.ac.uk/bertone/software")
+    (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
+                              "groups/bertone/software/HTqPCR.pdf"))
     (synopsis "Automated analysis of high-throughput qPCR data")
     (description
      "Analysis of Ct values from high throughput quantitative real-time
@@ -6993,14 +7007,14 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.2.0")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk"))))
+         "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7020,6 +7034,8 @@ a file-backed matrix with factor properties.")
        ("r-shinydashboard" ,r-shinydashboard)
        ("r-stringr" ,r-stringr)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/lindsayrutter/bigPint")
     (synopsis "Big multivariate data plotted interactively")
     (description
@@ -7294,14 +7310,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.12.4")
+    (version "1.12.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "01cnp00y5bk551c8gqgqp5468dvccg72i0rvh5cxgbx1c42zy6xn"))))
+         "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -7313,6 +7329,8 @@ access.")
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://waldronlab.io/MultiAssayExperiment/")
     (synopsis "Integration of multi-omics experiments in Bioconductor")
     (description
@@ -7397,18 +7415,19 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.4.0")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53"))))
+         "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocmanager" ,r-biocmanager)
+     `(("r-biocfilecache" ,r-biocfilecache)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-biocviews" ,r-biocviews)
        ("r-dplyr" ,r-dplyr)
        ("r-dt" ,r-dt)
@@ -7420,14 +7439,19 @@ gene selection, testing relationships, and so on.")
        ("r-igraph" ,r-igraph)
        ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
+       ("r-rappdirs" ,r-rappdirs)
        ("r-rbgl" ,r-rbgl)
        ("r-readr" ,r-readr)
        ("r-rex" ,r-rex)
+       ("r-rlang" ,r-rlang)
        ("r-rvest" ,r-rvest)
        ("r-stringr" ,r-stringr)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
+       ("r-tidyselect" ,r-tidyselect)
        ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/seandavi/BiocPkgTools")
     (synopsis "Collection of tools for learning about Bioconductor packages")
     (description
@@ -7474,14 +7498,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad"))))
+         "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -7495,6 +7519,8 @@ accessing web references for elements/sets are also available in BiocSet.")
        ("r-rstudioapi" ,r-rstudioapi)
        ("r-stringr" ,r-stringr)
        ("r-usethis" ,r-usethis)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
     (synopsis "Tools to aid the development of Bioconductor Workflow packages")
     (description