[PATCH] gnu: Add r-tricycle.

DoneSubmitted by Mădălin Ionel Patrașcu.
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2 participants
  • Mădălin Ionel Patrașcu
  • Ricardo Wurmus
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M
Mădălin Ionel Patrașcu wrote on 11 Apr 13:27 +0200
(address . guix-patches@gnu.org)
20220411112727.15262-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-tricycle): New variable.
---
gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)

Toggle diff (50 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce1e23f0bf..e6555c93df 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -775,6 +775,43 @@ (define-public r-ensdb-mmusculus-v79
 Ensembl.")
     (license license:artistic2.0)))
 
+(define-public r-tricycle
+  (package
+    (name "r-tricycle")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tricycle" version))
+              (sha256
+               (base32
+                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
+    (properties `((upstream-name . "tricycle")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-circular
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-iranges
+                             r-rcolorbrewer
+                             r-s4vectors
+                             r-scater
+                             r-scattermore
+                             r-singlecellexperiment
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hansenlab/tricycle")
+    (synopsis "Transferable representation and inference of cell cycle")
+    (description
+     "The package contains functions to infer and visualize cell cycle process
+using Single-cell RNA-Seq data.  It exploits the idea of transfer learning,
+projecting new data to the previous learned biologically interpretable space.
+The @code{tricycle} provides a pre-learned cell cycle space, which could be
+used to infer cell cycle time of human and mouse single cell samples.  In
+addition, it also offer functions to visualize cell cycle time on different
+embeddings and functions to build new reference.")
+    (license license:gpl3)))
+
 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
   (package
     (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
-- 
2.34.0
R
R
Ricardo Wurmus wrote on 14 Apr 06:59 +0200
(address . 54850-done@debbugs.gnu.org)
87h76wxnre.fsf@elephly.net
Applied, thanks!

In a subsequent commit I moved this definition, because it shouldn’t be
in the section reserved for annotation packages.

--
Ricardo
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