r-wgcna deps

2 files changed, 100 insertions, 9 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2bdf47a..dd7e77e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,27 +49,28 @@
   #:use-module (srfi srfi-1))
 
 (define-public r-wgcna
-  (let ((commit "9c68667c3"))
+  (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49"))
 (package
   (name "r-wgcna")
   (version (string-append "1.49-" commit))
   (source (origin
            (method git-fetch)
            (uri (git-reference
-                 (url "https://github.com/genenetwork/WGCNA.git")
+                 ;; (url "https://github.com/genenetwork/WGCNA.git")
+                 (url "https://github.com/pjotrp/WGCNA.git")
                  (commit commit)))
            (file-name (string-append name "-" commit))
            (sha256
             (base32
-             "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf581"))))
+             "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w"))))
   (properties `((upstream-name . "WGCNA")))
   (build-system r-build-system)
   (propagated-inputs
    `( ;; ("r-annotationdbi" ,r-annotationdbi)
      ; ("r-biocparallel" ,r-biocparallel)
-     ; ("r-dynamictreecut" ,r-dynamictreecut)
-     ; ("r-fastcluster" ,r-fastcluster)
-     ; ("r-foreach" ,r-foreach)
+     ("r-dynamictreecut" ,r-dynamictreecut)
+     ("r-fastcluster" ,r-fastcluster)
+     ("r-foreach" ,r-foreach)
      ; ("r-go-db" ,r-go-db)
      ; ("r-grdevices" ,r-grdevices)
      ; ("r-hmisc" ,r-hmisc)
@@ -85,9 +86,14 @@
   (home-page
     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
   (synopsis
-    "Weighted Correlation Network Analysis")
+    "Weighted gene correlation network analysis (wgcna)")
   (description
-    "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data.  Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits.  Also includes a number of utility functions for data manipulation and visualization.")
+    "Functions necessary to perform Weighted Correlation Network
+Analysis on high-dimensional data.  Includes functions for rudimentary
+data cleaning, construction of correlation networks, module
+identification, summarization, and relating of variables and modules
+to sample traits.  Also includes a number of utility functions for
+data manipulation and visualization.")
   (license license:gpl2+))))
 
 (define-public qtlreaper
@@ -123,7 +129,7 @@ test.  For the permutation test, it performs only as many permutations
 as are necessary to define the empirical P-value to a reasonable
 precision. It also performs bootstrap resampling to estimate the
 confidence region for the location of a putative QTL.")
-    (license license:gpl2)))
+    (license license:gpl2+)))
 
 (define-public plink2
   (package
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 2d83816..57ddfe6 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -39,6 +39,91 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-1))
 
+(define-public r-iterators
+(package
+  (name "r-iterators")
+  (version "1.0.8")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "iterators" version))
+      (sha256
+        (base32
+          "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
+  (build-system r-build-system)
+  ;; (propagated-inputs `(("r-utils" ,r-utils)))
+  (home-page
+    "http://cran.r-project.org/web/packages/iterators")
+  (synopsis "Provides Iterator Construct for R")
+  (description
+    "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.")
+  (license #f)))
+
+(define-public r-foreach
+(package
+  (name "r-foreach")
+  (version "1.4.3")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "foreach" version))
+      (sha256
+        (base32
+          "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
+  (build-system r-build-system)
+  (propagated-inputs `(("r-iterators" ,r-iterators)))
+  (home-page
+    "http://cran.r-project.org/web/packages/foreach")
+  (synopsis
+    "Provides Foreach Looping Construct for R")
+  (description
+    "Support for the foreach looping construct.  Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter.  This package in particular is intended to be used for its return value, rather than for its side effects.  In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function.  Using foreach without side effects also facilitates executing the loop in parallel.")
+  (license #f))
+)
+
+(define-public r-fastcluster
+(package
+  (name "r-fastcluster")
+  (version "1.1.16")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "fastcluster" version))
+      (sha256
+        (base32
+          "0x2prrsnqi5iqx23ki6y2agndjq8058ph6s703i4avrqi1q1w1q8"))))
+  (build-system r-build-system)
+  (home-page
+    "http://danifold.net/fastcluster.html")
+  (synopsis
+    "Fast Hierarchical Clustering Routines for R and Python")
+  (description
+    "This is a two-in-one package which provides interfaces to both R and Python.  It implements fast hierarchical, agglomerative clustering routines.  Part of the functionality is designed as drop-in replacement for existing routines: \"linkage\" in the SciPy package \"scipy.cluster.hierarchy\", \"hclust\" in R's \"stats\" package, and the \"flashClust\" package.  It provides the same functionality with the benefit of a much faster implementation.  Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.  For information on how to install the Python files, see the file INSTALL in the source distribution.")
+  (license #f)))
+
+(define-public r-dynamictreecut
+(package
+  (name "r-dynamictreecut")
+  (version "1.62")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "dynamicTreeCut" version))
+      (sha256
+        (base32
+          "1y11gg6k32wpsyb10kdv176ivczx2jlizs1xsrjrs6iwbncwzrkp"))))
+  (properties
+    `((upstream-name . "dynamicTreeCut")))
+  (build-system r-build-system)
+  ; (propagated-inputs `(("r-stats" ,r-stats)))
+  (home-page
+    "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
+  (synopsis
+    "Methods for detection of clusters in hierarchical clustering dendrograms.")
+  (description
+    "Contains methods for detection of clusters in hierarchical clustering dendrograms.")
+  (license license:gpl2+)))
+
 (define-public r-rcppeigen
 (package
   (name "r-rcppeigen")