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-rw-r--r--gnu/packages/bioconductor.scm49
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 67ee6079c6..f55416ef43 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1664,6 +1664,55 @@ expression and fold change can be easily seen with aid of the plots made with
the @code{GFAGpathUi} function.")
(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
+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")