* [bug#45399] [PATCH 01/10] gnu: r-sushi: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
` (8 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
---
gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 22 ----------------------
2 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 33f66ce8be..3dd34e7f24 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9300,3 +9300,25 @@ graph with the mapped data. In addition, @code{r-pathview} also seamlessly
integrates with pathway and gene set (enrichment) analysis tools for
large-scale and fully automated analysis.")
(license license:gpl3+)))
+
+(define-public r-sushi
+ (package
+ (name "r-sushi")
+ (version "1.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Sushi" version))
+ (sha256
+ (base32
+ "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
+ (properties `((upstream-name . "Sushi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biomart" ,r-biomart)
+ ("r-zoo" ,r-zoo)))
+ (home-page "https://bioconductor.org/packages/Sushi")
+ (synopsis "Tools for visualizing genomics data")
+ (description
+ "This package provides flexible, quantitative, and integrative genomic
+visualizations for publication-quality multi-panel figures.")
+ (license license:gpl2+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 96fa22f1a3..6ef93d9b62 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10867,28 +10867,6 @@ with your data.")
EMBL-EBI GWAS catalog.")
(license license:artistic2.0)))
-(define-public r-sushi
- (package
- (name "r-sushi")
- (version "1.28.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "Sushi" version))
- (sha256
- (base32
- "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
- (properties `((upstream-name . "Sushi")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biomart" ,r-biomart)
- ("r-zoo" ,r-zoo)))
- (home-page "https://bioconductor.org/packages/Sushi")
- (synopsis "Tools for visualizing genomics data")
- (description
- "This package provides flexible, quantitative, and integrative genomic
-visualizations for publication-quality multi-panel figures.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 02/10] gnu: r-gwascat: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
` (7 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 33 ---------------------------------
2 files changed, 33 insertions(+), 33 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3dd34e7f24..970602a32b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,39 @@ preprocessing of cytometry data, including i) normalization using bead
standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(license license:gpl2+)))
+(define-public r-gwascat
+ (package
+ (name "r-gwascat")
+ (version "2.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gwascat" version))
+ (sha256
+ (base32
+ "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocfilecache" ,r-biocfilecache)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-readr" ,r-readr)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-snpstats" ,r-snpstats)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/gwascat")
+ (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
+ (description
+ "This package provides tools for representing and modeling data in the
+EMBL-EBI GWAS catalog.")
+ (license license:artistic2.0)))
+
(define-public r-kegggraph
(package
(name "r-kegggraph")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6ef93d9b62..ab187dcddd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10834,39 +10834,6 @@ grid graphics package. This results in genomic information plotted together
with your data.")
(license license:artistic2.0)))
-(define-public r-gwascat
- (package
- (name "r-gwascat")
- (version "2.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gwascat" version))
- (sha256
- (base32
- "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-readr" ,r-readr)
- ("r-s4vectors" ,r-s4vectors)
- ("r-snpstats" ,r-snpstats)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/gwascat")
- (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
- (description
- "This package provides tools for representing and modeling data in the
-EMBL-EBI GWAS catalog.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 03/10] gnu: r-gviz: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
` (6 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
---
gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 49 ---------------------------------
2 files changed, 49 insertions(+), 49 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 970602a32b..11e9a46b11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,55 @@ preprocessing of cytometry data, including i) normalization using bead
standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(license license:gpl2+)))
+(define-public r-gviz
+ (package
+ (name "r-gviz")
+ (version "1.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Gviz" version))
+ (sha256
+ (base32
+ "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+ (properties `((upstream-name . "Gviz")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-digest" ,r-digest)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/Gviz")
+ (synopsis "Plotting data and annotation information along genomic coordinates")
+ (description
+ "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data. Gviz uses the biomaRt and the
+rtracklayer packages to perform live annotation queries to Ensembl and UCSC
+and translates this to e.g. gene/transcript structures in viewports of the
+grid graphics package. This results in genomic information plotted together
+with your data.")
+ (license license:artistic2.0)))
+
(define-public r-gwascat
(package
(name "r-gwascat")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab187dcddd..caa505fdab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10785,55 +10785,6 @@ interpretation of members of a collection of association statistics on a
family of feature/genome hypotheses.")
(license license:artistic2.0)))
-(define-public r-gviz
- (package
- (name "r-gviz")
- (version "1.34.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Gviz" version))
- (sha256
- (base32
- "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
- (properties `((upstream-name . "Gviz")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-bsgenome" ,r-bsgenome)
- ("r-digest" ,r-digest)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/Gviz")
- (synopsis "Plotting data and annotation information along genomic coordinates")
- (description
- "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data. Gviz uses the biomaRt and the
-rtracklayer packages to perform live annotation queries to Ensembl and UCSC
-and translates this to e.g. gene/transcript structures in viewports of the
-grid graphics package. This results in genomic information plotted together
-with your data.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (2 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
` (5 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
gnu/packages/bioconductor.scm | 56 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 56 ---------------------------------
2 files changed, 56 insertions(+), 56 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11e9a46b11..1bf9a49272 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,62 @@ preprocessing of cytometry data, including i) normalization using bead
standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(license license:gpl2+)))
+(define-public r-gqtlstats
+ (package
+ (name "r-gqtlstats")
+ (version "1.21.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gQTLstats" version))
+ (sha256
+ (base32
+ "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
+ (properties `((upstream-name . "gQTLstats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-batchjobs" ,r-batchjobs)
+ ("r-bbmisc" ,r-bbmisc)
+ ("r-beeswarm" ,r-beeswarm)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dplyr" ,r-dplyr)
+ ("r-erma" ,r-erma)
+ ("r-ffbase" ,r-ffbase)
+ ("r-foreach" ,r-foreach)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gqtlbase" ,r-gqtlbase)
+ ("r-hardyweinberg" ,r-hardyweinberg)
+ ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-mgcv" ,r-mgcv)
+ ("r-plotly" ,r-plotly)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-snpstats" ,r-snpstats)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/gQTLstats")
+ (synopsis "Computationally efficient analysis for eQTL and allied studies")
+ (description
+ "This package provides tools for the computationally efficient analysis
+of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
+The software in this package aims to support refinements and functional
+interpretation of members of a collection of association statistics on a
+family of feature/genome hypotheses.")
+ (license license:artistic2.0)))
+
(define-public r-gviz
(package
(name "r-gviz")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index caa505fdab..67b4c4cb73 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10729,62 +10729,6 @@ handling of existing population-level data for the purpose of flexibly
defining LD blocks.")
(license license:artistic2.0)))
-(define-public r-gqtlstats
- (package
- (name "r-gqtlstats")
- (version "1.21.3")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gQTLstats" version))
- (sha256
- (base32
- "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
- (properties `((upstream-name . "gQTLstats")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-batchjobs" ,r-batchjobs)
- ("r-bbmisc" ,r-bbmisc)
- ("r-beeswarm" ,r-beeswarm)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-erma" ,r-erma)
- ("r-ffbase" ,r-ffbase)
- ("r-foreach" ,r-foreach)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gqtlbase" ,r-gqtlbase)
- ("r-hardyweinberg" ,r-hardyweinberg)
- ("r-homo-sapiens" ,r-homo-sapiens)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-mgcv" ,r-mgcv)
- ("r-plotly" ,r-plotly)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-snpstats" ,r-snpstats)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/gQTLstats")
- (synopsis "Computationally efficient analysis for eQTL and allied studies")
- (description
- "This package provides tools for the computationally efficient analysis
-of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
-The software in this package aims to support refinements and functional
-interpretation of members of a collection of association statistics on a
-family of feature/genome hypotheses.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 05/10] gnu: r-ldblock: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (3 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
` (4 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
---
gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 34 ---------------------------------
2 files changed, 34 insertions(+), 34 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1bf9a49272..40a02dbe7f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9405,6 +9405,40 @@ maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.")
(license license:gpl2+)))
+(define-public r-ldblock
+ (package
+ (name "r-ldblock")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ldblock" version))
+ (sha256
+ (base32
+ "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-httr" ,r-httr)
+ ("r-matrix" ,r-matrix)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-snpstats" ,r-snpstats)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/ldblock")
+ (synopsis "Data structures for linkage disequilibrium measures in populations")
+ (description
+ "This package defines data structures for @dfn{linkage
+disequilibrium} (LD) measures in populations. Its purpose is to simplify
+handling of existing population-level data for the purpose of flexibly
+defining LD blocks.")
+ (license license:artistic2.0)))
+
(define-public r-pathview
(package
(name "r-pathview")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67b4c4cb73..25021f1ee8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10695,40 +10695,6 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
by Ernst and Kellis.")
(license license:artistic2.0)))
-(define-public r-ldblock
- (package
- (name "r-ldblock")
- (version "1.20.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ldblock" version))
- (sha256
- (base32
- "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-httr" ,r-httr)
- ("r-matrix" ,r-matrix)
- ("r-rsamtools" ,r-rsamtools)
- ("r-snpstats" ,r-snpstats)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/ldblock")
- (synopsis "Data structures for linkage disequilibrium measures in populations")
- (description
- "This package defines data structures for @dfn{linkage
-disequilibrium} (LD) measures in populations. Its purpose is to simplify
-handling of existing population-level data for the purpose of flexibly
-defining LD blocks.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 06/10] gnu: r-erma: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (4 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: " zimoun
` (3 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 40 ---------------------------------
2 files changed, 40 insertions(+), 40 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 40a02dbe7f..466bb71101 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,46 @@ preprocessing of cytometry data, including i) normalization using bead
standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(license license:gpl2+)))
+(define-public r-erma
+ (package
+ (name "r-erma")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "erma" version))
+ (sha256
+ (base32
+ "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-iranges" ,r-iranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/erma")
+ (synopsis "Epigenomic road map adventures")
+ (description
+ "The epigenomics road map describes locations of epigenetic marks in DNA
+from a variety of cell types. Of interest are locations of histone
+modifications, sites of DNA methylation, and regions of accessible chromatin.
+This package presents a selection of elements of the road map including
+metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
+by Ernst and Kellis.")
+ (license license:artistic2.0)))
+
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 25021f1ee8..1c59d7a690 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10655,46 +10655,6 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
several related annotation packages.")
(license license:artistic2.0)))
-(define-public r-erma
- (package
- (name "r-erma")
- (version "1.6.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "erma" version))
- (sha256
- (base32
- "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-homo-sapiens" ,r-homo-sapiens)
- ("r-iranges" ,r-iranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/erma")
- (synopsis "Epigenomic road map adventures")
- (description
- "The epigenomics road map describes locations of epigenetic marks in DNA
-from a variety of cell types. Of interest are locations of histone
-modifications, sites of DNA methylation, and regions of accessible chromatin.
-This package presents a selection of elements of the road map including
-metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
-by Ernst and Kellis.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (5 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
` (2 subsequent siblings)
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 32 --------------------------------
2 files changed, 27 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 466bb71101..3b8dce30e5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-homo-sapiens
+ (package
+ (name "r-homo-sapiens")
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
+ (sha256
+ (base32
+ "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
+ (properties
+ `((upstream-name . "Homo.sapiens")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-go-db" ,r-go-db)
+ ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+ ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
+ ("r-organismdbi" ,r-organismdbi)
+ ("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/Homo.sapiens/")
+ (synopsis "Annotation package for the Homo.sapiens object")
+ (description
+ "This package contains the Homo.sapiens object to access data from
+several related annotation packages.")
+ (license license:artistic2.0)))
+
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c59d7a690..2a6ac38505 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10623,38 +10623,6 @@ and more.")
the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(license license:gpl3)))
-(define-public r-homo-sapiens
- (package
- (name "r-homo-sapiens")
- (version "1.3.1")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "Homo.sapiens_"
- version ".tar.gz"))
- (sha256
- (base32
- "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
- (properties
- `((upstream-name . "Homo.sapiens")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)
- ("r-go-db" ,r-go-db)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
- ("r-organismdbi" ,r-organismdbi)
- ("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://bioconductor.org/packages/Homo.sapiens/")
- (synopsis "Annotation package for the Homo.sapiens object")
- (description
- "This package contains the Homo.sapiens object to access data from
-several related annotation packages.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 08/10] gnu: r-snpstats: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (6 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 10/10] gnu: r-ggbio: " zimoun
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3b8dce30e5..ff9e26bbde 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9540,6 +9540,33 @@ integrates with pathway and gene set (enrichment) analysis tools for
large-scale and fully automated analysis.")
(license license:gpl3+)))
+(define-public r-snpstats
+ (package
+ (name "r-snpstats")
+ (version "1.40.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "snpStats" version))
+ (sha256
+ (base32
+ "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
+ (properties `((upstream-name . "snpStats")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-matrix" ,r-matrix)
+ ("r-survival" ,r-survival)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/snpStats")
+ (synopsis "Methods for SNP association studies")
+ (description
+ "This package provides classes and statistical methods for large
+@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
+the earlier snpMatrix package, allowing for uncertainty in genotypes.")
+ (license license:gpl3)))
+
(define-public r-sushi
(package
(name "r-sushi")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2a6ac38505..76236929de 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10596,33 +10596,6 @@ of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
and more.")
(license license:artistic2.0)))
-(define-public r-snpstats
- (package
- (name "r-snpstats")
- (version "1.40.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "snpStats" version))
- (sha256
- (base32
- "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
- (properties `((upstream-name . "snpStats")))
- (build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-matrix" ,r-matrix)
- ("r-survival" ,r-survival)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/snpStats")
- (synopsis "Methods for SNP association studies")
- (description
- "This package provides classes and statistical methods for large
-@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
-the earlier snpMatrix package, allowing for uncertainty in genotypes.")
- (license license:gpl3)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (7 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
@ 2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 10/10] gnu: r-ggbio: " zimoun
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 47 ---------------------------------
2 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ff9e26bbde..a3dd93e763 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
by Ernst and Kellis.")
(license license:artistic2.0)))
+(define-public r-gqtlbase
+ (package
+ (name "r-gqtlbase")
+ (version "1.21.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gQTLBase" version))
+ (sha256
+ (base32
+ "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
+ (properties `((upstream-name . "gQTLBase")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; This is an upstream bug.
+ (add-after 'unpack 'fix-imports
+ (lambda _
+ (substitute* "NAMESPACE"
+ ((".*maxffmode.*") "")
+ (("importFrom\\(ff,.*") "import(ff)\n"))
+ #t)))))
+ (propagated-inputs
+ `(("r-batchjobs" ,r-batchjobs)
+ ("r-bbmisc" ,r-bbmisc)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-bit" ,r-bit)
+ ("r-doparallel" ,r-doparallel)
+ ("r-ff" ,r-ff)
+ ("r-ffbase" ,r-ffbase)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/gQTLBase")
+ (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+ (description
+ "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+ (license license:artistic2.0)))
+
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76236929de..bc483e6f13 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10549,53 +10549,6 @@ views. High-level plots include sequence fragment length, edge-linked
interval to data view, mismatch pileup, and several splicing summaries.")
(license license:artistic2.0)))
-(define-public r-gqtlbase
- (package
- (name "r-gqtlbase")
- (version "1.21.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gQTLBase" version))
- (sha256
- (base32
- "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
- (properties `((upstream-name . "gQTLBase")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; This is an upstream bug.
- (add-after 'unpack 'fix-imports
- (lambda _
- (substitute* "NAMESPACE"
- ((".*maxffmode.*") "")
- (("importFrom\\(ff,.*") "import(ff)\n"))
- #t)))))
- (propagated-inputs
- `(("r-batchjobs" ,r-batchjobs)
- ("r-bbmisc" ,r-bbmisc)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-bit" ,r-bit)
- ("r-doparallel" ,r-doparallel)
- ("r-ff" ,r-ff)
- ("r-ffbase" ,r-ffbase)
- ("r-foreach" ,r-foreach)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/gQTLBase")
- (synopsis "Infrastructure for eQTL, mQTL and similar studies")
- (description
- "The purpose of this package is to simplify the storage and interrogation
-of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
-and more.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
^ permalink raw reply related [flat|nested] 14+ messages in thread* [bug#45399] [PATCH 10/10] gnu: r-ggbio: Move to (gnu packages bioconductor).
2020-12-23 18:06 ` zimoun
` (8 preceding siblings ...)
2020-12-23 18:06 ` [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: " zimoun
@ 2020-12-23 18:06 ` zimoun
9 siblings, 0 replies; 14+ messages in thread
From: zimoun @ 2020-12-23 18:06 UTC (permalink / raw)
To: 45399
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
---
gnu/packages/bioconductor.scm | 65 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 65 ---------------------------------
2 files changed, 65 insertions(+), 65 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a3dd93e763..55df9bf7d1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
by Ernst and Kellis.")
(license license:artistic2.0)))
+(define-public r-ggbio
+ (package
+ (name "r-ggbio")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ggbio" version))
+ (sha256
+ (base32
+ "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; See https://github.com/tengfei/ggbio/issues/117
+ ;; This fix will be included in the next release.
+ (add-after 'unpack 'fix-typo
+ (lambda _
+ (substitute* "R/GGbio-class.R"
+ (("fechable") "fetchable"))
+ #t)))))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggally" ,r-ggally)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtable" ,r-gtable)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-organismdbi" ,r-organismdbi)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "http://www.tengfei.name/ggbio/")
+ (synopsis "Visualization tools for genomic data")
+ (description
+ "The ggbio package extends and specializes the grammar of graphics for
+biological data. The graphics are designed to answer common scientific
+questions, in particular those often asked of high throughput genomics data.
+All core Bioconductor data structures are supported, where appropriate. The
+package supports detailed views of particular genomic regions, as well as
+genome-wide overviews. Supported overviews include ideograms and grand linear
+views. High-level plots include sequence fragment length, edge-linked
+interval to data view, mismatch pileup, and several splicing summaries.")
+ (license license:artistic2.0)))
+
(define-public r-gqtlbase
(package
(name "r-gqtlbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc483e6f13..512abcd8fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10484,71 +10484,6 @@ high-level packages for biological data visualization. This saves development
effort and encourages consistency.")
(license license:artistic2.0)))
-(define-public r-ggbio
- (package
- (name "r-ggbio")
- (version "1.38.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ggbio" version))
- (sha256
- (base32
- "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; See https://github.com/tengfei/ggbio/issues/117
- ;; This fix will be included in the next release.
- (add-after 'unpack 'fix-typo
- (lambda _
- (substitute* "R/GGbio-class.R"
- (("fechable") "fetchable"))
- #t)))))
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-bsgenome" ,r-bsgenome)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggally" ,r-ggally)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-gtable" ,r-gtable)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-organismdbi" ,r-organismdbi)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "http://www.tengfei.name/ggbio/")
- (synopsis "Visualization tools for genomic data")
- (description
- "The ggbio package extends and specializes the grammar of graphics for
-biological data. The graphics are designed to answer common scientific
-questions, in particular those often asked of high throughput genomics data.
-All core Bioconductor data structures are supported, where appropriate. The
-package supports detailed views of particular genomic regions, as well as
-genome-wide overviews. Supported overviews include ideograms and grand linear
-views. High-level plots include sequence fragment length, edge-linked
-interval to data view, mismatch pileup, and several splicing summaries.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
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