(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
45f15f5a52814fed81e54bce8b044fbd@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-seraster): New variable.
* gnu/packages/cran.scm (r-rearrr): New variable.
[Patch] gnu: Add r-seraster and r-rearrr.
- Open
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Dale Mellor
- M?d?lin Ionel Patra?cu
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
M
M
[PATCH 1/2] gnu: Add r-rearrr.
(address . 70536@debbugs.gnu.org)
023204df1edfba5ec5057df74aaf43b5afca6b14.1713879129.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-rearrr): New variable.
Change-Id: I41e06b24e565a4070f570b7fd5c656f185aacfa9
---
gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
Toggle diff (44 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ee0aac7f7a..83ba5f2a0d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4259,6 +4259,35 @@ (define-public r-readxl
;; 'rapidxml' which is Boost.
(license (list license:gpl3 license:bsd-2 license:boost1.0))))
+(define-public r-rearrr
+ (package
+ (name "r-rearrr")
+ (version "0.3.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rearrr" version))
+ (sha256
+ (base32 "1inx1gikiqxaf6a8g10b02l1qs2y0zxs2yrxn6dyx9n6xlra3rnr"))))
+ (properties `((upstream-name . "rearrr")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-checkmate
+ r-dplyr
+ r-lifecycle
+ r-plyr
+ r-purrr
+ r-r6
+ r-rlang
+ r-tibble))
+ (home-page "https://github.com/ludvigolsen/rearrr")
+ (synopsis "Rearranging data by a set of methods")
+ (description
+ "This package arranges data by a set of methods. It uses rearrangers to
+reorder data points and mutators to change their values. From basic utilities,
+to centering the greatest value, to swirling in 3-dimensional space, rearrr
+enables creativity when plotting and experimenting with data.")
+ (license license:expat)))
+
(define-public r-model4you
(package
(name "r-model4you")
base-commit: 2d19e505f6f9f82aebc9ba8c74ba223818acd9bc
--
2.41.0
M
[PATCH 2/2] gnu: Add r-seraster.
(address . 70536@debbugs.gnu.org)
0d6e1fd7ee69b9b9751145ee2dfb039f913e0800.1713879129.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-seraster): New variable.
Change-Id: I345dcbdfba23b34f122d7c193604cf950fe0d8f0
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
Toggle diff (53 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fca094977..828d9cfe36 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11025,6 +11025,46 @@ (define-public r-seqpattern
reference point and sorted by a user defined feature.")
(license license:gpl3+)))
+;; This is not a Bioconductor package but it depends on three packages.
+(define-public r-seraster
+ ;; There are no tags or releases.
+ (let ((commit "4fdc1ffe5d3feb65de9880329d221cf276b393a1")
+ (revision "1"))
+ (package
+ (name "r-seraster")
+ (version (git-version "0.99.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JEFworks-Lab/SEraster")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0y33lk8q0h9nfzmf7slxxvw3l0djassp4l63nsjpm3p6z4pah5s4"))))
+ (properties `((upstream-name . "SEraster")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocparallel
+ r-ggplot2
+ r-matrix
+ r-rearrr
+ r-sf
+ r-spatialexperiment
+ r-summarizedexperiment))
+ (home-page "https://github.com/JEFworks-Lab/SEraster")
+ (synopsis
+ "Rasterization framework for scalable spatial omics data analysis")
+ (description "SEraster is a rasterization preprocessing framework that
+aggregates cellular information into spatial pixels to reduce resource requirements
+for spatial omics data analysis. This package reduces the number of points in
+spatial omics datasets for downstream analysis through a process of rasterization
+where single cells gene expression or cell-type labels are aggregated into equally
+sized pixels based on a user-defined resolution. SEraster can be incorporated
+with other packages to conduct downstream analyses for spatial omics datasets,
+such as detecting spatially variable genes.")
+ (license license:gpl3))))
+
(define-public r-sesame
(package
(name "r-sesame")
--
2.41.0
M
[PATCH 2/2] v2 gnu: Add r-seraster.
(address . 70536@debbugs.gnu.org)
79ede4754c5753d845573ed8b4c09e8f44ce00c1.1713882185.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-seraster): New variable.
Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
Toggle diff (54 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa6bce5591..514d01c87f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13159,6 +13159,45 @@ (define-public r-seqgl
factors bound at the specific regions.")
(license license:gpl2+)))
+(define-public r-seraster
+ ;; There are no tags or releases.
+ (let ((commit "4fdc1ffe5d3feb65de9880329d221cf276b393a1")
+ (revision "1"))
+ (package
+ (name "r-seraster")
+ (version (git-version "0.99.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JEFworks-Lab/SEraster")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0y33lk8q0h9nfzmf7slxxvw3l0djassp4l63nsjpm3p6z4pah5s4"))))
+ (properties `((upstream-name . "SEraster")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biocparallel
+ r-ggplot2
+ r-matrix
+ r-rearrr
+ r-sf
+ r-spatialexperiment
+ r-summarizedexperiment))
+ (home-page "https://github.com/JEFworks-Lab/SEraster")
+ (synopsis
+ "Rasterization framework for scalable spatial omics data analysis")
+ (description
+ "This package is a rasterization preprocessing framework that aggregates
+cellular information into spatial pixels to reduce resource requirements for
+spatial omics data analysis. SEraster reduces the number of points in spatial
+omics datasets for downstream analysis through a process of rasterization where
+single cells gene expression or cell-type labels are aggregated into equally
+sized pixels based on a user-defined resolution. SEraster can be incorporated
+with other packages to conduct downstream analyses for spatial omics datasets,
+such as detecting spatially variable genes.")
+ (license license:gpl3))))
+
(define-public emboss
(package
(name "emboss")
base-commit: 2d19e505f6f9f82aebc9ba8c74ba223818acd9bc
--
2.41.0
D
[PATCH 0/2] gnu: Add r-seraster and r-rearrr.
(address . 70536@debbugs.gnu.org)
0248f5c9814df2ba8ad85286a251a1c2e314c442.camel@rdmp.org
This is needed to put a title in qa.guix.gnu.org/patches.
?