GNU bug report logs - #55148
[PATCH] gnu: Add r-agilp.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-agilp.
Date: Wed, 27 Apr 2022 14:50:15 +0200

* gnu/packages/bioconductor.scm (r-agilp): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 67ee6079c6..c0d874b423 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1664,6 +1664,50 @@ (define-public r-adamgui
 the @code{GFAGpathUi} function.")
     (license license:gpl2+)))
 
+(define-public r-agilp
+  (package
+    (name "r-agilp")
+    (version "3.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "agilp" version))
+              (sha256
+               (base32
+                "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp"))))
+    (properties `((upstream-name . "agilp")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/agilp")
+    (synopsis "Processing of Agilent expression array")
+    (description
+      "This package @code{agilp} was developed to provide a pipeline for the
+low-level analysis of gene expression microarray data, primarily focused on the
+Agilent platform, but which also provides utilities which may be useful for
+other platforms.  @code{Agilp} implements functions like:
+@itemize
+@item
+@code{AAProcess}: extracts raw expression data from Agilent expression array
+scanner files;
+@item
+@code{filenamex}: a file name listing utility;
+@item
+@code{Baseline}: constructs a file with the mean of each probe from a set of raw
+expression array data files
+@item
+@code{Loader}: selects a set of processed array files from directory according
+to criteria from a template file;
+@item
+@code{AALoess}: normalises a set of gene expression data files using @code{LOESS}
+against a reference data set;
+@item
+@code{IDswop}: maps expression data across different bioinformatic identifiers;
+@item
+@code{Equaliser}: trims a set of gene expression data files to include only the
+set of identifiers common to all files.
+@end itemize")
+    ;; Some files are under GPLv2+ but the combined work is released under the
+    ;; GPLv3.
+    (license license:gpl3)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")

base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76
-- 
2.34.0

Message #10 received at 55148-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 55148-done <at> debbugs.gnu.org
Subject: Re: [bug#55148] [PATCH] gnu: Add r-agilp.
Date: Wed, 27 Apr 2022 16:36:42 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-agilp): New variable.

Thank you.  I applied it after trimming the description, because all
that detail was probably a little much.

-- 
Ricardo

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