GNU bug report logs - #68381
[PATCH] gnu: Add r-azimuth.

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

From: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-azimuth.
Date: Thu, 11 Jan 2024 11:20:43 +0000

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

Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03
---
 gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f574fea0e9..9b45c54ef9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11171,6 +11171,66 @@ (define-public r-archr
        "This package is designed to streamline scATAC analyses in R.")
       (license license:gpl2+))))
 
+(define-public r-azimuth
+  (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e")
+        (revision "1"))
+    (package
+      (name "r-azimuth")
+      (version (git-version "0.5.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/satijalab/azimuth")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm"))))
+      (properties `((upstream-name . "Azimuth")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38
+                               r-dt
+                               r-ensdb-hsapiens-v86
+                               r-future
+                               r-ggplot2
+                               r-glmgampoi
+                               r-googlesheets4
+                               r-hdf5r
+                               r-htmltools
+                               r-httr
+                               r-jaspar2020
+                               r-jsonlite
+                               r-matrix
+                               r-patchwork
+                               r-plotly
+                               r-presto
+                               r-rcpp
+                               r-rlang
+                               r-scales
+                               r-seurat
+                               r-seuratdata
+                               r-seuratdisk
+                               r-seuratobject
+                               r-shiny
+                               r-shinybs
+                               r-shinydashboard
+                               r-shinyjs
+                               r-signac
+                               r-stringr
+                               r-tfbstools
+                               r-withr))
+      (home-page "https://github.com/satijalab/azimuth")
+      (synopsis
+       "Shiny app showcasing a single-cell data query-reference mapping algorithm")
+      (description "Azimuth utilizes an annotated reference dataset.
+It automates the processing, analysis, and interpretation.
+This applies specifically to new single-cell RNA-seq or
+ATAC-seq experiments.  Azimuth leverages a reference-based
+mapping pipeline that inputs acounts matrix and performs
+normalization, visualization, cell annotation, and
+differential expression.")
+      (license license:gpl3))))
+
 (define-public r-icellnet
   ;; v1.0 tagged in 2020, last commit contains many fixes.
   ;; DESCRIPTION says Version: 0.0.0.9000.

base-commit: 6341dddcb9e7c8d555ea7294d61dcf64d775e032
-- 
2.34.1

Message #10 received at 68381-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 68381-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-azimuth.
Date: Fri, 12 Jan 2024 13:40:38 +0100

Applied, thank you!

-- 
Ricardo

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