GNU bug report logs - #60955
[PATCH] gnu: Add r-scds.

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

From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-scds.
Date: Fri, 20 Jan 2023 09:28:06 +0100

* gnu/packages/bioconductor.scm (r-scds): New variable.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm |  2 +-
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 53c7d048c9..0699813af3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet <at> gmail.com>
+;;; Copyright © 2023 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7266,6 +7267,33 @@ (define-public r-scannotatr
 cell types based on specific research needs.")
     (license license:expat)))
 
+(define-public r-scds
+  (package
+    (name "r-scds")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scds" version))
+              (sha256
+               (base32
+                "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd"))))
+    (properties `((upstream-name . "scds")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dplyr
+                             r-matrix
+                             r-proc
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scds")
+    (synopsis "In-silico doublet annotation for single cell RNA sequencing data")
+    (description
+     "This is an R package for doublet annotation of single cell RNA sequencing data.  
+@code{scds} provides methods to annotate doublets in scRNA-seq data computationally.")
+    (license license:expat)))
+
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 152771a645..533f8a5f27 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
-;;; Copyright © 2022 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
+;;; Copyright © 2022,2023 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
-- 
2.34.1

Message #8 received at 60955 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>, 60955 <at> debbugs.gnu.org,
 rekado <at> elephly.net
Subject: Re: [bug#60955] [PATCH] gnu: Add r-scds.
Date: Tue, 24 Jan 2023 19:37:51 +0100

Hi Ricardo,

On Fri, 20 Jan 2023 at 09:28, Navid Afkhami <navid.afkhami <at> mdc-berlin.de> wrote:
> * gnu/packages/bioconductor.scm (r-scds): New variable.
> ---
>  gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
>  gnu/packages/bioinformatics.scm |  2 +-
>  2 files changed, 29 insertions(+), 1 deletion(-)

In case you have missed your colleague’s patch. :-)


Cheers,
simon

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