[PATCH 0/2] Add r-htqpcr and r-unifiedwmwqpcr.

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2 participants
  • Ludovic Courtès
  • zimoun
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unassigned
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zimoun
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normal
Z
Z
zimoun wrote on 8 Oct 2019 18:53
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20191008165307.903-1-zimon.toutoune@gmail.com
Dear,

These patches add two BioConductor packages.

The licenses are compliant with the ones find in the file 'DESCRIPTION' but
`guix build' reports:

installing 0 license files from '.'


All the best,
simon


zimoun (2):
gnu: Add r-htqpcr.
gnu: Add r-unifiedwmwqpcr.

gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)

--
2.21.0
Z
Z
zimoun wrote on 8 Oct 2019 19:35
[PATCH 1/2] gnu: Add r-htqpcr.
(address . 37666@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20191008173518.1074-1-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-htqpcr): New variable.
---
gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)

Toggle diff (51 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7b0405427c..4fc4ffbce2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,6 +2,7 @@
;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -6048,3 +6049,36 @@ attributable to individual, tissue, time point, or technical variables. The
package includes dream differential expression analysis for repeated
measures.")
(license license:gpl2+)))
+
+(define-public r-htqpcr
+ (package
+ (name "r-htqpcr")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HTqPCR" version))
+ (sha256
+ (base32
+ "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
+ (properties `((upstream-name . "HTqPCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-gplots" ,r-gplots)
+ ("r-limma" ,r-limma)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://www.ebi.ac.uk/bertone/software")
+ (synopsis "Automated analysis of high-throughput qPCR data")
+ (description
+ "Analysis of Ct values from high throughput quantitative real-time
+PCR (qPCR) assays across multiple conditions or replicates. The input data
+can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
+OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
+Laboratories; conventional 96- or 384-well plates; or microfluidic devices
+such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
+loading, quality assessment, normalization, visualization and parametric or
+non-parametric testing for statistical significance in Ct values between
+features (e.g. genes, microRNAs).")
+ (license license:artistic2.0)))
--
2.21.0
Z
Z
zimoun wrote on 8 Oct 2019 19:35
[PATCH 1/1] gnu: Add r-unifiedwmwqpcr.
(address . 37666@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20191008173518.1074-2-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fc4ffbce2..9cd36fc69c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6082,3 +6082,28 @@ loading, quality assessment, normalization, visualization and parametric or
non-parametric testing for statistical significance in Ct values between
features (e.g. genes, microRNAs).")
(license license:artistic2.0)))
+
+(define-public r-unifiedwmwqpcr
+ (package
+ (name "r-unifiedwmwqpcr")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "unifiedWMWqPCR" version))
+ (sha256
+ (base32
+ "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
+ (properties
+ `((upstream-name . "unifiedWMWqPCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-htqpcr" ,r-htqpcr)))
+ (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
+ (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
+ (description
+ "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR
+data. This modified test allows for testing differential expression in qPCR
+data.")
+ (license license:gpl2+)))
--
2.21.0
Z
Z
zimoun wrote on 8 Oct 2019 19:35
[PATCH 2/2] gnu: Add r-unifiedwmwqpcr.
(address . 37666@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20191008173518.1074-3-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fc4ffbce2..9cd36fc69c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6082,3 +6082,28 @@ loading, quality assessment, normalization, visualization and parametric or
non-parametric testing for statistical significance in Ct values between
features (e.g. genes, microRNAs).")
(license license:artistic2.0)))
+
+(define-public r-unifiedwmwqpcr
+ (package
+ (name "r-unifiedwmwqpcr")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "unifiedWMWqPCR" version))
+ (sha256
+ (base32
+ "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
+ (properties
+ `((upstream-name . "unifiedWMWqPCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-htqpcr" ,r-htqpcr)))
+ (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
+ (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
+ (description
+ "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR
+data. This modified test allows for testing differential expression in qPCR
+data.")
+ (license license:gpl2+)))
--
2.21.0
L
L
Ludovic Courtès wrote on 15 Oct 2019 14:13
Re: [bug#37666] [PATCH 1/2] gnu: Add r-htqpcr.
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 37666-done@debbugs.gnu.org)
875zkqw6iz.fsf@gnu.org
Hello!

zimoun <zimon.toutoune@gmail.com> skribis:

Toggle quote (2 lines)
> * gnu/packages/bioconductor.scm (r-htqpcr): New variable.

[...]

Toggle quote (2 lines)
> * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable.

Applied, thanks! :-)

Ludo’.
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