* [bug#47010] [PATCH 02/10] gnu: r-deseq2: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
@ 2021-03-08 17:57 ` zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 03/10] gnu: r-dexseq: " zimoun
` (6 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:57 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 38 ---------------------------------
2 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e15984d0e3..f2dd4bb70b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1487,6 +1487,44 @@ structure.")
microarrays.")
(license license:artistic2.0)))
+(define-public r-deseq2
+ (package
+ (name "r-deseq2")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq2" version))
+ (sha256
+ (base32
+ "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
+ (properties `((upstream-name . "DESeq2")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-locfit" ,r-locfit)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DESeq2")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides functions to estimate variance-mean dependence in
+count data from high-throughput nucleotide sequencing assays and test for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:lgpl3+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 258c3ca409..64585127e6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,44 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-deseq2
- (package
- (name "r-deseq2")
- (version "1.30.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DESeq2" version))
- (sha256
- (base32
- "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
- (properties `((upstream-name . "DESeq2")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-locfit" ,r-locfit)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/DESeq2")
- (synopsis "Differential gene expression analysis")
- (description
- "This package provides functions to estimate variance-mean dependence in
-count data from high-throughput nucleotide sequencing assays and test for
-differential expression based on a model using the negative binomial
-distribution.")
- (license license:lgpl3+)))
-
(define-public r-dexseq
(package
(name "r-dexseq")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 02/10] gnu: r-deseq2: " zimoun
@ 2021-03-08 17:57 ` zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 04/10] gnu: r-annotationforge: " zimoun
` (5 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:57 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 45 ---------------------------------
2 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f2dd4bb70b..883b6df2fb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1525,6 +1525,51 @@ differential expression based on a model using the negative binomial
distribution.")
(license license:lgpl3+)))
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64585127e6..4fa4a1e354 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,51 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-dexseq
- (package
- (name "r-dexseq")
- (version "1.36.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DEXSeq" version))
- (sha256
- (base32
- "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
- (properties `((upstream-name . "DEXSeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biomart" ,r-biomart)
- ("r-deseq2" ,r-deseq2)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-statmod" ,r-statmod)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/DEXSeq")
- (synopsis "Inference of differential exon usage in RNA-Seq")
- (description
- "This package is focused on finding differential exon usage using RNA-seq
-exon counts between samples with different experimental designs. It provides
-functions that allows the user to make the necessary statistical tests based
-on a model that uses the negative binomial distribution to estimate the
-variance between biological replicates and generalized linear models for
-testing. The package also provides functions for the visualization and
-exploration of the results.")
- (license license:gpl3+)))
-
(define-public r-annotationforge
(package
(name "r-annotationforge")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 04/10] gnu: r-annotationforge: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 02/10] gnu: r-deseq2: " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 03/10] gnu: r-dexseq: " zimoun
@ 2021-03-08 17:57 ` zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 05/10] gnu: r-rbgl: " zimoun
` (4 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:57 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 32 --------------------------------
2 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 883b6df2fb..706b87b207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1487,6 +1487,38 @@ structure.")
microarrays.")
(license license:artistic2.0)))
+(define-public r-annotationforge
+ (package
+ (name "r-annotationforge")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationForge" version))
+ (sha256
+ (base32
+ "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
+ (properties
+ `((upstream-name . "AnnotationForge")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/AnnotationForge")
+ (synopsis "Code for building annotation database packages")
+ (description
+ "This package provides code for generating Annotation packages and their
+databases. Packages produced are intended to be used with AnnotationDbi.")
+ (license license:artistic2.0)))
+
(define-public r-deseq2
(package
(name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4fa4a1e354..3212641af9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,38 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-annotationforge
- (package
- (name "r-annotationforge")
- (version "1.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "AnnotationForge" version))
- (sha256
- (base32
- "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
- (properties
- `((upstream-name . "AnnotationForge")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/AnnotationForge")
- (synopsis "Code for building annotation database packages")
- (description
- "This package provides code for generating Annotation packages and their
-databases. Packages produced are intended to be used with AnnotationDbi.")
- (license license:artistic2.0)))
-
(define-public r-rbgl
(package
(name "r-rbgl")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 05/10] gnu: r-rbgl: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
` (2 preceding siblings ...)
2021-03-08 17:57 ` [bug#47010] [PATCH 04/10] gnu: r-annotationforge: " zimoun
@ 2021-03-08 17:57 ` zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 06/10] gnu: r-gseabase: " zimoun
` (3 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:57 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
---
gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 23 -----------------------
2 files changed, 23 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 706b87b207..0a9dc4f9ba 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1650,6 +1650,29 @@ high-throughput sequencing experiments.")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-rbgl
+ (package
+ (name "r-rbgl")
+ (version "1.66.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RBGL" version))
+ (sha256
+ (base32
+ "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
+ (properties `((upstream-name . "RBGL")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-graph" ,r-graph)))
+ (home-page "https://www.bioconductor.org/packages/RBGL")
+ (synopsis "Interface to the Boost graph library")
+ (description
+ "This package provides a fairly extensive and comprehensive interface to
+the graph algorithms contained in the Boost library.")
+ (license license:artistic2.0)))
+
(define-public r-regioner
(package
(name "r-regioner")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3212641af9..0f96ffc02e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,29 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-rbgl
- (package
- (name "r-rbgl")
- (version "1.66.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "RBGL" version))
- (sha256
- (base32
- "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
- (properties `((upstream-name . "RBGL")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-graph" ,r-graph)))
- (home-page "https://www.bioconductor.org/packages/RBGL")
- (synopsis "Interface to the Boost graph library")
- (description
- "This package provides a fairly extensive and comprehensive interface to
-the graph algorithms contained in the Boost library.")
- (license license:artistic2.0)))
-
(define-public r-gseabase
(package
(name "r-gseabase")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 06/10] gnu: r-gseabase: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
` (3 preceding siblings ...)
2021-03-08 17:57 ` [bug#47010] [PATCH 05/10] gnu: r-rbgl: " zimoun
@ 2021-03-08 17:57 ` zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 07/10] gnu: r-category: " zimoun
` (2 subsequent siblings)
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:57 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 29 -----------------------------
2 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0a9dc4f9ba..a17c6beeef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1630,6 +1630,35 @@ exploration of the results.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-gseabase
+ (package
+ (name "r-gseabase")
+ (version "1.52.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GSEABase" version))
+ (sha256
+ (base32
+ "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
+ (properties `((upstream-name . "GSEABase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-graph" ,r-graph)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GSEABase")
+ (synopsis "Gene set enrichment data structures and methods")
+ (description
+ "This package provides classes and methods to support @dfn{Gene Set
+Enrichment Analysis} (GSEA).")
+ (license license:artistic2.0)))
+
(define-public r-hpar
(package
(name "r-hpar")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f96ffc02e..23b8ce6892 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,35 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-gseabase
- (package
- (name "r-gseabase")
- (version "1.52.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "GSEABase" version))
- (sha256
- (base32
- "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
- (properties `((upstream-name . "GSEABase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-graph" ,r-graph)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/GSEABase")
- (synopsis "Gene set enrichment data structures and methods")
- (description
- "This package provides classes and methods to support @dfn{Gene Set
-Enrichment Analysis} (GSEA).")
- (license license:artistic2.0)))
-
(define-public r-category
(package
(name "r-category")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 07/10] gnu: r-category: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
` (4 preceding siblings ...)
2021-03-08 17:57 ` [bug#47010] [PATCH 06/10] gnu: r-gseabase: " zimoun
@ 2021-03-08 17:58 ` zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 08/10] gnu: r-gostats: " zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 09/10] gnu: r-shortread: " zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:58 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a17c6beeef..4e3dd25d61 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1519,6 +1519,37 @@ microarrays.")
databases. Packages produced are intended to be used with AnnotationDbi.")
(license license:artistic2.0)))
+(define-public r-category
+ (package
+ (name "r-category")
+ (version "2.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Category" version))
+ (sha256
+ (base32
+ "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
+ (properties `((upstream-name . "Category")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-graph" ,r-graph)
+ ("r-gseabase" ,r-gseabase)
+ ("r-matrix" ,r-matrix)
+ ("r-rbgl" ,r-rbgl)
+ ("r-dbi" ,r-dbi)))
+ (home-page "https://bioconductor.org/packages/Category")
+ (synopsis "Category analysis")
+ (description
+ "This package provides a collection of tools for performing category
+analysis.")
+ (license license:artistic2.0)))
+
(define-public r-deseq2
(package
(name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 23b8ce6892..6b32f3416c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,37 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-category
- (package
- (name "r-category")
- (version "2.56.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Category" version))
- (sha256
- (base32
- "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
- (properties `((upstream-name . "Category")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genefilter" ,r-genefilter)
- ("r-graph" ,r-graph)
- ("r-gseabase" ,r-gseabase)
- ("r-matrix" ,r-matrix)
- ("r-rbgl" ,r-rbgl)
- ("r-dbi" ,r-dbi)))
- (home-page "https://bioconductor.org/packages/Category")
- (synopsis "Category analysis")
- (description
- "This package provides a collection of tools for performing category
-analysis.")
- (license license:artistic2.0)))
-
(define-public r-gostats
(package
(name "r-gostats")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 08/10] gnu: r-gostats: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
` (5 preceding siblings ...)
2021-03-08 17:58 ` [bug#47010] [PATCH 07/10] gnu: r-category: " zimoun
@ 2021-03-08 17:58 ` zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 09/10] gnu: r-shortread: " zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:58 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e3dd25d61..4f4088db27 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1661,6 +1661,37 @@ exploration of the results.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-gostats
+ (package
+ (name "r-gostats")
+ (version "2.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GOstats" version))
+ (sha256
+ (base32
+ "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
+ (properties `((upstream-name . "GOstats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationforge" ,r-annotationforge)
+ ("r-biobase" ,r-biobase)
+ ("r-category" ,r-category)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-rgraphviz" ,r-rgraphviz)
+ ("r-rbgl" ,r-rbgl)))
+ (home-page "https://bioconductor.org/packages/GOstats")
+ (synopsis "Tools for manipulating GO and microarrays")
+ (description
+ "This package provides a set of tools for interacting with GO and
+microarray data. A variety of basic manipulation tools for graphs, hypothesis
+testing and other simple calculations.")
+ (license license:artistic2.0)))
+
(define-public r-gseabase
(package
(name "r-gseabase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6b32f3416c..186b051865 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,37 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-gostats
- (package
- (name "r-gostats")
- (version "2.56.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "GOstats" version))
- (sha256
- (base32
- "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
- (properties `((upstream-name . "GOstats")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationforge" ,r-annotationforge)
- ("r-biobase" ,r-biobase)
- ("r-category" ,r-category)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rbgl" ,r-rbgl)))
- (home-page "https://bioconductor.org/packages/GOstats")
- (synopsis "Tools for manipulating GO and microarrays")
- (description
- "This package provides a set of tools for interacting with GO and
-microarray data. A variety of basic manipulation tools for graphs, hypothesis
-testing and other simple calculations.")
- (license license:artistic2.0)))
-
(define-public r-shortread
(package
(name "r-shortread")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread* [bug#47010] [PATCH 09/10] gnu: r-shortread: Move to (gnu packages bioconductor).
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
` (6 preceding siblings ...)
2021-03-08 17:58 ` [bug#47010] [PATCH 08/10] gnu: r-gostats: " zimoun
@ 2021-03-08 17:58 ` zimoun
7 siblings, 0 replies; 12+ messages in thread
From: zimoun @ 2021-03-08 17:58 UTC (permalink / raw)
To: 47010; +Cc: zimoun
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 ---------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4088db27..05077b422e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-shortread
+ (package
+ (name "r-shortread")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ShortRead" version))
+ (sha256
+ (base32
+ "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+ (properties `((upstream-name . "ShortRead")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/ShortRead")
+ (synopsis "FASTQ input and manipulation tools")
+ (description
+ "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report. Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes. The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 186b051865..fda4516052 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,49 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-shortread
- (package
- (name "r-shortread")
- (version "1.48.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ShortRead" version))
- (sha256
- (base32
- "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
- (properties `((upstream-name . "ShortRead")))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/ShortRead")
- (synopsis "FASTQ input and manipulation tools")
- (description
- "This package implements sampling, iteration, and input of FASTQ files.
-It includes functions for filtering and trimming reads, and for generating a
-quality assessment report. Data are represented as
-@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
-purposes. The package also contains legacy support for early single-end,
-ungapped alignment formats.")
- (license license:artistic2.0)))
-
(define-public r-systempiper
(package
(name "r-systempiper")
--
2.30.1
^ permalink raw reply related [flat|nested] 12+ messages in thread