From a45dfa8a731c9ba2626ee7ca19e7d61f2e82925d Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 26 Apr 2022 13:36:23 +0200 Subject: gnu: Add r-adimpute. * gnu/packages/bioconductor.scm (r-adimpute): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') 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") -- cgit v1.2.3 ='msg-avail'>...* guix/scripts/system.scm (show-help, %docker-format-options, %options, %default-options, show-docker-format-options, show-docker-format-options/detailed, process-action): Handle '--max-layers' option. * gnu/system/image.scm (system-docker-image): Same. * gnu/image.scm (<image>)[max-layers]: New record field. Change-Id: I2726655aefd6688b976057fd5a38e9972ebfc292 Oleg Pykhalov 2022-09-24system: image: Add wsl2 support....* gnu/image.scm (<image>)[format]: Add wsl2 support. * gnu/system/image.scm (wsl2-image, wsl2-image-type): New variables. (image->root-file-system): Add wsl2 image support. (system-image): Ditto. Alex Griffin 2022-09-24system: image: Add tarball support....* gnu/image.scm (<image>)[fields]: Add tarball to the supported formats. * gnu/system/image.scm (tarball-image, tarball-image-type): New variables. (system-tarball-image): New procedure. (image->root-file-system): Add tarball image support. (system-image): Ditto. * doc/guix.texi ("System Images"): Document it. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Alex Griffin 2022-09-24image: Make the operating-system field mandatory....Make the operating-system field mandatory as creating an image without it makes no sense. Introduce a new macro, image-without-os for the specific cases where the image is only created to be inherited from afterwards. * gnu/image.scm (<image>)[operating-system]: Make it mandatory. * gnu/system/image.scm (image-without-os): New macro. (efi-disk-image, efi32-disk-image, iso9660-image, docker-image, raw-with-offset-disk-image): Use it. * gnu/system/images/hurd.scm (hurd-disk-image): Ditto. Mathieu Othacehe 2022-09-07image: Use #true and #false....* gnu/image.scm: Use #true and #false instead of #t and #f respectively. No functional change. Mathieu Othacehe 2022-09-07image: Use a default size partition value....* gnu/image.scm (<partition>)[size]: Default to 'guess like the image record. Mathieu Othacehe 2022-08-31image: Add comments....* gnu/image.scm: Add some comments across the whole module. Mathieu Othacehe 2022-08-30image: Remove an unused field....* gnu/image.scm (<partition>)[device]: Remove it. Mathieu Othacehe 2022-08-30image: Perform more sanitizing....* gnu/image.scm (validate-size, validate-partition-offset, validate-partition-flags): New macros. (<partition>)[size, offset, flags]: Sanitize those fields using the above procedures respectively. Mathieu Othacehe 2022-07-01image: Add sanitizers for 'format' and 'partition-table-type'....This allows common mistakes to be diagnosed early. * gnu/image.scm (define-set-sanitizer): New macro. (validate-image-format, validate-partition-table-type): New sanitizers. (<image>)[format, partition-table-type]: Add 'sanitize' property. Ludovic Courtès 2022-07-01image: Add default value for partition initializer....Previously, the default value would lead to a wrong-type-to-apply crash. * gnu/system/image.scm (system-disk-image)[image-builder]: When 'partition-initializer' returns #f, fall back to INITIALIZE-ROOT-PARTITION. * gnu/tests/base.scm (run-root-unmount-test)[test-image]: Remove 'initializer' field of partition. * gnu/image.scm (<partition>)[initializer]: Add comment. Ludovic Courtès