GNU bug report logs - #55124
[PATCH] gnu: Add r-adimpute and r-saver

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

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-adimpute and r-saver
Date: Tue, 26 Apr 2022 11:33:40 +0000

[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Message #8 received at 55124 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <55124 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-adimpute.
Date: Tue, 26 Apr 2022 13:36:23 +0200

* gnu/packages/bioconductor.scm (r-adimpute): New variable.
---
 gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fa862d736f..a861c2e576 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1616,6 +1616,54 @@ (define-public r-adam
 functionally associated genes} (GFAG).")
     (license license:gpl2+)))
 
+(define-public r-adimpute
+  (package
+    (name "r-adimpute")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ADImpute" version))
+              (sha256
+               (base32
+                "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2"))))
+    (properties `((upstream-name . "ADImpute")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocparallel
+                             r-checkmate
+                             r-data-table
+                             r-drimpute
+                             r-kernlab
+                             r-mass
+                             r-matrix
+                             r-rsvd
+                             r-s4vectors
+                             r-saver
+                             r-singlecellexperiment
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ADImpute")
+    (synopsis "Adaptive computational prediction for dropout imputations")
+    (description
+     "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically unable
+to quantify the expression levels of all genes in a cell, creating a need for
+the computational prediction of missing values (dropout imputation).  Most
+existing dropout imputation methods are limited in the sense that they
+exclusively use the scRNA-seq dataset at hand and do not exploit external
+gene-gene relationship information.  The @code{ADImpute} package proposes two
+novel methods to address this issue:
+
+@enumerate
+@item a gene regulatory network-based approach using gene-gene relationships
+learnt from external data;
+@item a baseline approach corresponding to a sample-wide average.
+@end enumerate
+
+@code{ADImpute} implements these novel methods and also combines them with
+existing imputation methods like @code{DrImpute} and @code{SAVER}.
+@code{ADImpute} can learn the best performing method per gene and combine the
+results from different methods into an ensemble.")
+    (license license:gpl3+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.34.0

Message #11 received at 55124 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <55124 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-saver.
Date: Tue, 26 Apr 2022 13:36:22 +0200

* gnu/packages/cran.scm (r-saver): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 21cfca3102..ab93a94158 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2333,6 +2333,37 @@ (define-public r-sass
 language, which is stable, powerful, and CSS compatible.")
     (license license:expat)))
 
+(define-public r-saver
+  (package
+    (name "r-saver")
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "SAVER" version))
+              (sha256
+               (base32
+                "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
+    (properties `((upstream-name . "SAVER")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-doparallel r-foreach r-glmnet r-iterators
+                             r-matrix))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mohuangx/SAVER")
+    (synopsis
+     "Recovery of the gene expression profile in noisy and sparse scRNA-seq data")
+    (description
+     "This package is an implementation of a regularized regression prediction
+and empirical Bayes method to recover the true gene expression profile in noisy
+and sparse single-cell RNA-seq data.  In @dfn{single-cell RNA sequencing}
+(scRNA-seq) studies, only a small fraction of the transcripts present in each
+cell are sequenced.  This leads to unreliable quantification of genes with low
+or moderate expression, which hinders downstream analysis.  This package
+@dfn{single-cell analysis via expression recovery} (SAVER) implements an
+expression recovery method for unique molecule index (UMI)-based scRNA-seq data
+that borrows information across genes and cells to provide accurate expression
+estimates for all genes.")
+    (license license:gpl2)))
+
 ;; This package includes minified JavaScript files.  When upgrading please
 ;; check that there are no new minified JavaScript files.
 (define-public r-bslib

base-commit: 30ff557bd7255dddec16f4a032e58f5a88d5e448
-- 
2.34.0

Message #16 received at 55124-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 55124-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-adimpute and r-saver
Date: Wed, 27 Apr 2022 15:51:30 +0200

Thanks for the patches.  I applied them with minor stylistic changes.

-- 
Ricardo

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