[PATCH] Add r-motifrg.

[PATCH] Add r-motifrg.

[Ricardo Wurmus]

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From 82d9056a23f72d87aa8baa90398695aefea55879 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 18 Mar 2016 12:16:17 +0100
Subject: [PATCH] gnu: Add r-motifrg.

* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
---
 gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7692361..23d427e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4827,6 +4827,33 @@ Stephens (1990).")
 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-motifrg
+  (package
+    (name "r-motifrg")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "motifRG" version))
+       (sha256
+        (base32
+         "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn"))))
+    (properties `((upstream-name . "motifRG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-iranges" ,r-iranges)
+       ("r-seqlogo" ,r-seqlogo)
+       ("r-xvector" ,r-xvector)))
+    (home-page "http://bioconductor.org/packages/motifRG")
+    (synopsis "Discover motifs in high throughput sequencing data")
+    (description
+     "This package provides tools for discriminative motif discovery in high
+throughput genetic sequencing data sets using regression methods.")
+    (license license:artistic2.0)))
+
 (define-public r-qtl
  (package
   (name "r-qtl")
-- 
2.1.0

Re: [PATCH] Add r-motifrg.

[Leo Famulari]

On Wed, Apr 06, 2016 at 05:33:24PM +0200, Ricardo Wurmus wrote:
> From 82d9056a23f72d87aa8baa90398695aefea55879 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 18 Mar 2016 12:16:17 +0100
> Subject: [PATCH] gnu: Add r-motifrg.
> 
> * gnu/packages/bioinformatics.scm (r-motifrg): New variable.

LGTM!

I'm curious, is this for finding patterns "fuzzily"? Is that what is
meant by motif?

> ---
>  gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 7692361..23d427e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4827,6 +4827,33 @@ Stephens (1990).")
>  by UCSC (hg19, February 2009) and stored in Biostrings objects.")
>      (license license:artistic2.0)))
>  
> +(define-public r-motifrg
> +  (package
> +    (name "r-motifrg")
> +    (version "1.14.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (bioconductor-uri "motifRG" version))
> +       (sha256
> +        (base32
> +         "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn"))))
> +    (properties `((upstream-name . "motifRG")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +     `(("r-biostrings" ,r-biostrings)
> +       ("r-bsgenome" ,r-bsgenome)
> +       ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
> +       ("r-iranges" ,r-iranges)
> +       ("r-seqlogo" ,r-seqlogo)
> +       ("r-xvector" ,r-xvector)))
> +    (home-page "http://bioconductor.org/packages/motifRG")
> +    (synopsis "Discover motifs in high throughput sequencing data")
> +    (description
> +     "This package provides tools for discriminative motif discovery in high
> +throughput genetic sequencing data sets using regression methods.")
> +    (license license:artistic2.0)))
> +
>  (define-public r-qtl
>   (package
>    (name "r-qtl")
> -- 
> 2.1.0
> 
> 

Re: [PATCH] Add r-motifrg.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Wed, Apr 06, 2016 at 05:33:24PM +0200, Ricardo Wurmus wrote:
>> From 82d9056a23f72d87aa8baa90398695aefea55879 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Fri, 18 Mar 2016 12:16:17 +0100
>> Subject: [PATCH] gnu: Add r-motifrg.
>> 
>> * gnu/packages/bioinformatics.scm (r-motifrg): New variable.
>
> LGTM!
>
> I'm curious, is this for finding patterns "fuzzily"? Is that what is
> meant by motif?

A sequence motif is a pattern of nucleotides, and they are notated in a
similar fashion to regular expressions for text.  Unlike regular
expressions, they are mostly used to describe a recurring or conserved
pattern, not so much to search for it.  Sequence logos are a graphical
representation of such motifs or sequence patterns, indicating possible
sequences and the relative frequency of each possible letter.

~~ Ricardo