gnu: r-wgcna: Move to (gnu packages bioconductor).

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 57da0a9..6842444 100644 (file)
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9279,14 +9279,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.15.1")
+    (version "0.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
+         "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)
@@ -9971,14 +9971,14 @@ This package provides an R interface.")
 (define-public r-rcpphnsw
   (package
     (name "r-rcpphnsw")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppHNSW" version))
        (sha256
         (base32
-         "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
+         "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
     (properties `((upstream-name . "RcppHNSW")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -10125,14 +10125,14 @@ to colexicographical order.")
 (define-public r-misc3d
   (package
     (name "r-misc3d")
-    (version "0.8-4")
+    (version "0.9-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "misc3d" version))
        (sha256
         (base32
-         "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
+         "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/misc3d/")
     (synopsis "Miscellaneous 3D Plots")
@@ -10968,14 +10968,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
+         "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -11935,13 +11935,13 @@ Differences with other sparse matrix packages are:
 (define-public r-fields
   (package
     (name "r-fields")
-    (version "10.3")
+    (version "11.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fields" version))
        (sha256
-        (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
+        (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-maps" ,r-maps)
@@ -12200,14 +12200,14 @@ JASA, 94:496-509.")
 (define-public r-etm
   (package
     (name "r-etm")
-    (version "1.1")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "etm" version))
        (sha256
         (base32
-         "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
+         "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
@@ -12855,20 +12855,22 @@ transformation, respectively.")
 (define-public r-shinyjs
   (package
     (name "r-shinyjs")
-    (version "1.1")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyjs" version))
        (sha256
         (base32
-         "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
+         "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
        ("r-htmltools" ,r-htmltools)
        ("r-jsonlite" ,r-jsonlite)
        ("r-shiny" ,r-shiny)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://deanattali.com/shinyjs")
     (synopsis "Improve the user experience of your Shiny apps")
     (description
@@ -13889,14 +13891,14 @@ sampling.")
 (define-public r-deldir
   (package
     (name "r-deldir")
-    (version "0.1-28")
+    (version "0.1-29")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deldir" version))
        (sha256
         (base32
-         "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
+         "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/deldir")
@@ -13913,14 +13915,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.9-5")
+    (version "0.9-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
+         "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
@@ -14475,44 +14477,6 @@ authoring books and technical documents with R Markdown.")
 that accept short and long options.")
     (license license:gpl2+)))
 
-(define-public r-wgcna
-  (package
-    (name "r-wgcna")
-    (version "1.69")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "WGCNA" version))
-       (sha256
-        (base32
-         "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
-    (properties `((upstream-name . "WGCNA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dynamictreecut" ,r-dynamictreecut)
-       ("r-fastcluster" ,r-fastcluster)
-       ("r-foreach" ,r-foreach)
-       ("r-go-db" ,r-go-db)
-       ("r-hmisc" ,r-hmisc)
-       ("r-impute" ,r-impute)
-       ("r-rcpp" ,r-rcpp)
-       ("r-survival" ,r-survival)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-preprocesscore" ,r-preprocesscore)))
-    (home-page
-     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
-    (synopsis "Weighted correlation network analysis")
-    (description
-     "This package provides functions necessary to perform Weighted
-Correlation Network Analysis on high-dimensional data.  It includes functions
-for rudimentary data cleaning, construction and summarization of correlation
-networks, module identification and functions for relating both variables and
-modules to sample traits.  It also includes a number of utility functions for
-data manipulation and visualization.")
-    (license license:gpl2+)))
-
 (define-public r-kernlab
   (package
     (name "r-kernlab")
@@ -16098,14 +16062,14 @@ been used in the call to @code{aov}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.3.1.1")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
+         "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16690,14 +16654,14 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
+         "0ldxgcayyisp2gcbv4xw9zpb48bp4czi8016kq5nqdqhv1qb3sz0"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16838,14 +16802,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.8.2")
+    (version "0.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
+         "1vax5p1znq2ddbks2i614hbrnn2x6x71942xx49p813qk8dh284l"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18156,14 +18120,14 @@ models.")
 (define-public r-gamlss
   (package
     (name "r-gamlss")
-    (version "5.1-7")
+    (version "5.2-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gamlss" version))
        (sha256
         (base32
-         "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
+         "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
     (properties `((upstream-name . "gamlss")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20305,14 +20269,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
 (define-public r-forecast
   (package
     (name "r-forecast")
-    (version "8.12")
+    (version "8.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "forecast" version))
        (sha256
         (base32
-         "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
+         "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
     (properties `((upstream-name . "forecast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22479,14 +22443,14 @@ multi-state models.")
 (define-public r-scatterpie
   (package
     (name "r-scatterpie")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterpie" version))
        (sha256
         (base32
-         "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
+         "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
     (properties `((upstream-name . "scatterpie")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22573,50 +22537,6 @@ Try a demo of the LSD by running @code{demotour()}.")
     ;; Either version
     (license (list license:gpl2 license:gpl3))))
 
-(define-public r-fourcseq
-  (package
-    (name "r-fourcseq")
-    (version "1.22.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "FourCSeq" version))
-       (sha256
-        (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
-    (properties `((upstream-name . "FourCSeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biostrings" ,r-biostrings)
-       ("r-deseq2" ,r-deseq2)
-       ("r-fda" ,r-fda)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gtools" ,r-gtools)
-       ("r-lsd" ,r-lsd)
-       ("r-matrix" ,r-matrix)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page
-     "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
-    (synopsis "Analysis of multiplexed 4C sequencing data")
-    (description
-     "This package is an R package dedicated to the analysis of (multiplexed)
-4C sequencing data.  @code{r-fourcseq} provides a pipeline to detect specific
-interactions between DNA elements and identify differential interactions
-between conditions.  The statistical analysis in R starts with individual bam
-files for each sample as inputs.  To obtain these files, the package contains
-a Python script to demultiplex libraries and trim off primer sequences.  With
-a standard alignment software the required bam files can be then be
-generated.")
-    (license license:gpl3+)))
-
 (define-public r-phylogram
   (package
     (name "r-phylogram")
@@ -23216,14 +23136,14 @@ aggregation for comparing different implementations in order to provide a
 (define-public r-rfast
   (package
     (name "r-rfast")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rfast" version))
        (sha256
         (base32
-         "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
+         "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
     (properties `((upstream-name . "Rfast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24435,18 +24355,17 @@ as allowing spectra with different resolutions.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.2.0")
+    (version "3.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+                "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-cluster" ,r-cluster)
+     `(("r-cluster" ,r-cluster)
        ("r-cowplot" ,r-cowplot)
        ("r-fitdistrplus" ,r-fitdistrplus)
        ("r-future" ,r-future)
@@ -24464,6 +24383,7 @@ as allowing spectra with different resolutions.")
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
        ("r-miniui" ,r-miniui)
        ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
@@ -24528,14 +24448,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.")
 (define-public r-diversitree
   (package
     (name "r-diversitree")
-    (version "0.9-13")
+    (version "0.9-14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "diversitree" version))
         (sha256
          (base32
-          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+          "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))