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[09/18] gnu: Add r-wgcna.

Message ID 20161124165139.13740-10-rekado@elephly.net
State New
Headers show

Commit Message

Ricardo Wurmus Nov. 24, 2016, 4:51 p.m. UTC
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

Comments

Ben Woodcroft Nov. 25, 2016, 10:38 a.m. UTC | #1
On 25/11/16 02:51, Ricardo Wurmus wrote:
> [..]
> +    (home-page
> +     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
This line is a bit long, I don't remember, should it be split over two 
lines?

> +    (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 of correlation networks, module
> +identification, summarization, and relating of variables and modules to sample
I found the 'and' a bit confusing. Maybe:

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.

> +traits.  It also includes a number of utility functions for data manipulation
> +and visualization.")
> +    (license license:gpl2+)))
> +
>   (define-public emboss
>     (package
>       (name "emboss")
LGTM, I have one just like it locally.
ben
Ricardo Wurmus Nov. 28, 2016, 9:45 p.m. UTC | #2
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> On 25/11/16 02:51, Ricardo Wurmus wrote:
>> [..]
>> +    (home-page
>> +     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
> This line is a bit long, I don't remember, should it be split over two 
> lines?

True, but I left it as it is.  It’s just a tiny bit too long and we
don’t usually split home-page strings, so I opted to keep it like this.

>> +    (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 of correlation networks, module
>> +identification, summarization, and relating of variables and modules to sample
> I found the 'and' a bit confusing. Maybe:
>
> 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.

Thanks for the improved sentence.  I’ve updated the description.

>> +traits.  It also includes a number of utility functions for data manipulation
>> +and visualization.")
>> +    (license license:gpl2+)))
>> +
>>   (define-public emboss
>>     (package
>>       (name "emboss")
> LGTM, I have one just like it locally.
> ben

Cool, thanks for the review!
diff mbox

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 254ee13..7bcac59 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7449,6 +7449,42 @@  characterization and visualization of a wide range of mutational patterns
 in SNV base substitution data.")
     (license license:expat)))
 
+(define-public r-wgcna
+  (package
+    (name "r-wgcna")
+    (version "1.51")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "WGCNA" version))
+       (sha256
+        (base32
+         "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+    (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-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 of correlation networks, module
+identification, summarization, and relating of variables and modules to sample
+traits.  It also includes a number of utility functions for data manipulation
+and visualization.")
+    (license license:gpl2+)))
+
 (define-public emboss
   (package
     (name "emboss")