* [bug#58827] [PATCH] gnu: Add r-dama and r-damefinder.
@ 2022-10-28 2:49 MadalinIonel.Patrascu
2022-10-28 2:53 ` [bug#58827] [PATCH 1/2] gnu: Add r-dama Mădălin Ionel Patrașcu
0 siblings, 1 reply; 4+ messages in thread
From: MadalinIonel.Patrascu @ 2022-10-28 2:49 UTC (permalink / raw)
To: 58827
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* gnu/packages/bioconductor.scm ( r-dama and r-damefinder): New variables.
Unrelated patches, added in the alphabetical order.
All the best,
Mădălin-Ionel!
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^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#58827] [PATCH 1/2] gnu: Add r-dama.
2022-10-28 2:49 [bug#58827] [PATCH] gnu: Add r-dama and r-damefinder MadalinIonel.Patrascu
@ 2022-10-28 2:53 ` Mădălin Ionel Patrașcu
2022-10-28 2:53 ` [bug#58827] [PATCH 2/2] gnu: Add r-damefinder Mădălin Ionel Patrașcu
2022-10-28 13:13 ` bug#58827: [PATCH 1/2] gnu: Add r-dama Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-28 2:53 UTC (permalink / raw)
To: 58827; +Cc: rekado
* gnu/packages/bioconductor.scm (r-dama): New variable.
---
gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..9f79954d8d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3013,6 +3013,29 @@ (define-public r-cummerbund
used visualizations.")
(license license:artistic2.0)))
+(define-public r-dama
+ (package
+ (name "r-dama")
+ (version "1.68.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "daMA" version))
+ (sha256
+ (base32
+ "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m"))))
+ (properties `((upstream-name . "daMA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-mass))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html")
+ ;; http://www.microarrays.med.uni-goettingen.de - domain not found
+ (synopsis
+ "Efficient design and analysis of factorial two-colour microarray data")
+ (description
+ "This package contains functions for the efficient design of factorial two-
+colour microarray experiments and for the statistical analysis of factorial
+microarray data.")
+ (license license:gpl2+)))
+
(define-public r-dearseq
(package
(name "r-dearseq")
base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260
--
2.38.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#58827] [PATCH 2/2] gnu: Add r-damefinder.
2022-10-28 2:53 ` [bug#58827] [PATCH 1/2] gnu: Add r-dama Mădălin Ionel Patrașcu
@ 2022-10-28 2:53 ` Mădălin Ionel Patrașcu
2022-10-28 13:13 ` bug#58827: [PATCH 1/2] gnu: Add r-dama Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-28 2:53 UTC (permalink / raw)
To: 58827; +Cc: rekado
* gnu/packages/bioconductor.scm (r-damefinder): New variable.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f79954d8d..81918e4fe6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3036,6 +3036,47 @@ (define-public r-dama
microarray data.")
(license license:gpl2+)))
+(define-public r-damefinder
+ (package
+ (name "r-damefinder")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DAMEfinder" version))
+ (sha256
+ (base32
+ "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf"))))
+ (properties `((upstream-name . "DAMEfinder")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biostrings
+ r-bumphunter
+ r-cowplot
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-limma
+ r-plyr
+ r-readr
+ r-reshape2
+ r-rsamtools
+ r-s4vectors
+ r-stringr
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/DAMEfinder")
+ (synopsis "Differential allelicly methylated regions")
+ (description
+ "This package offers functionality for taking methtuple or @code{bismark}
+outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and compute
+@acronym{DAMEs, Differential Allelicly MEthylated regions}. It also offers nice
+visualization of methyl-circle plots.")
+ (license license:expat)))
+
(define-public r-dearseq
(package
(name "r-dearseq")
--
2.38.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#58827: [PATCH 1/2] gnu: Add r-dama.
2022-10-28 2:53 ` [bug#58827] [PATCH 1/2] gnu: Add r-dama Mădălin Ionel Patrașcu
2022-10-28 2:53 ` [bug#58827] [PATCH 2/2] gnu: Add r-damefinder Mădălin Ionel Patrașcu
@ 2022-10-28 13:13 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2022-10-28 13:13 UTC (permalink / raw)
To: Mădălin Ionel Patrașcu; +Cc: 58827-done
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
> * gnu/packages/bioconductor.scm (r-dama): New variable.
Applied, thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
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