GNU bug report logs - #70536
[Patch] gnu: Add r-seraster and r-rearrr.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: [Patch] gnu: Add r-seraster and r-rearrr.
Date: Tue, 23 Apr 2024 13:29:43 +0000

[Message part 1 (text/plain, inline)]

* gnu/packages/bioconductor.scm (r-seraster): New variable.

* gnu/packages/cran.scm (r-rearrr): New variable.

[Message part 2 (text/html, inline)]

Message #8 received at 70536 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70536 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-rearrr.
Date: Tue, 23 Apr 2024 15:32:08 +0200

* gnu/packages/cran.scm (r-rearrr): New variable.

Change-Id: I41e06b24e565a4070f570b7fd5c656f185aacfa9
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

Message #11 received at 70536 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70536 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-seraster.
Date: Tue, 23 Apr 2024 15:32:09 +0200

* gnu/packages/bioconductor.scm (r-seraster): New variable.

Change-Id: I345dcbdfba23b34f122d7c193604cf950fe0d8f0
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

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

Message #14 received at 70536 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70536 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] v2 gnu: Add r-seraster.
Date: Tue, 23 Apr 2024 16:23:05 +0200

* gnu/packages/bioinformatics.scm (r-seraster): New variable.

Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

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

Message #17 received at 70536 <at> debbugs.gnu.org (full text, mbox):

From: Dale Mellor <guix-devel-0brg6a <at> rdmp.org>
To: 70536 <at> debbugs.gnu.org
Subject: [PATCH 0/2] gnu: Add r-seraster and r-rearrr.
Date: Tue, 23 Apr 2024 22:44:14 +0100

This is needed to put a title in qa.guix.gnu.org/patches.

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