[bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection.

[bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.
---
 gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36c9db90bd..86d65d2031 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7986,6 +7986,46 @@ (define-public r-chromunity
 Pore-C concatemers.")
       (license license:gpl3))))
 
+(define-public r-doubletcollection
+  (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd")
+        (revision "1"))
+    (package
+      (name "r-doubletcollection")
+      (version (git-version "1.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/xnnba1984/DoubletCollection")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "02cvibyc2nwc4037ramm5cskjwyrb9ib9hkrfhmvhbslkn5ixz1v"))))
+      (properties `((upstream-name . "DoubletCollection")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biocgenerics
+                               r-doubletfinder
+                               r-gam
+                               r-ggplot2
+                               r-ggthemes
+                               r-mast
+                               r-mclust
+                               r-prroc
+                               r-reticulate
+                               r-scales
+                               r-scdblfinder
+                               r-scds
+                               r-seurat
+                               r-singlecellexperiment
+                               r-slingshot
+                               r-summarizedexperiment))
+      (home-page "https://github.com/xnnba1984/DoubletCollection")
+      (synopsis "Tool for finding doublets in scRNA-seq data")
+      (description
+       "This is an R package that integrates the installation of doublet-detection methods.  
+In addition, this tool is used for execution and benchmark of those eight mentioned methods.")
+      (license license:gpl3+))))
+
 (define-public r-pando
   (package
     (name "r-pando")
-- 
2.34.1

[bug#60958] [PATCH 2/2] gnu: Add r-scds.

[Navid Afkhami]

* 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 93c6165b62..bdbdeecc35 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
+;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7678,6 +7679,33 @@ (define-public r-trajectoryutils
 structures to hold pseudotime inference results.")
     (license license:gpl3)))
 
+(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-slingshot
   (package
    (name "r-slingshot")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 86d65d2031..70ac252a8c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
-;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
+;;; Copyright © 2022,2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
-- 
2.34.1

bug#60957: [PATCH 1/2] gnu: Add r-doubletcollection.

[Ricardo Wurmus]

Thanks for the patch.  Applied!

-- 
Ricardo

bug#60958: [PATCH 2/2] gnu: Add r-scds.

[Ricardo Wurmus]

Thanks for the patch!

I trimmed off the changes to bioinformatics.scm and moved the change to
the copyright line to patch #60958 where you modified that file.

Applied!

-- 
Ricardo