* [bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection.
@ 2023-01-20 8:57 Navid Afkhami
2023-01-20 8:58 ` [bug#60958] [PATCH 2/2] gnu: Add r-scds Navid Afkhami
2023-01-20 10:07 ` bug#60957: [PATCH 1/2] gnu: Add r-doubletcollection Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: Navid Afkhami @ 2023-01-20 8:57 UTC (permalink / raw)
To: 60957
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#60958] [PATCH 2/2] gnu: Add r-scds.
2023-01-20 8:57 [bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection Navid Afkhami
@ 2023-01-20 8:58 ` Navid Afkhami
2023-01-20 10:08 ` bug#60958: " Ricardo Wurmus
2023-01-20 10:07 ` bug#60957: [PATCH 1/2] gnu: Add r-doubletcollection Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Navid Afkhami @ 2023-01-20 8:58 UTC (permalink / raw)
To: 60958
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#60957: [PATCH 1/2] gnu: Add r-doubletcollection.
2023-01-20 8:57 [bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection Navid Afkhami
2023-01-20 8:58 ` [bug#60958] [PATCH 2/2] gnu: Add r-scds Navid Afkhami
@ 2023-01-20 10:07 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2023-01-20 10:07 UTC (permalink / raw)
To: 60957-done
Thanks for the patch. Applied!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2023-01-20 10:10 UTC | newest]
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2023-01-20 8:57 [bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection Navid Afkhami
2023-01-20 8:58 ` [bug#60958] [PATCH 2/2] gnu: Add r-scds Navid Afkhami
2023-01-20 10:08 ` bug#60958: " Ricardo Wurmus
2023-01-20 10:07 ` bug#60957: [PATCH 1/2] gnu: Add r-doubletcollection Ricardo Wurmus
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