From unknown Tue Aug 19 10:01:17 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#55124 <55124@debbugs.gnu.org> To: bug#55124 <55124@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-adimpute and r-saver Reply-To: bug#55124 <55124@debbugs.gnu.org> Date: Tue, 19 Aug 2025 17:01:17 +0000 retitle 55124 [PATCH] gnu: Add r-adimpute and r-saver reassign 55124 guix-patches submitter 55124 "MadalinIonel.Patrascu@mdc-berlin.de" severity 55124 normal tag 55124 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 07:33:52 2022 Received: (at submit) by debbugs.gnu.org; 26 Apr 2022 11:33:52 +0000 Received: from localhost ([127.0.0.1]:37266 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJS3-00006X-L6 for submit@debbugs.gnu.org; Tue, 26 Apr 2022 07:33:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:60792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJS2-00005a-8B for submit@debbugs.gnu.org; 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--_000_7d2f41e893ea40a98618c962d4f02ca5mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 07:36:44 2022 Received: (at 55124) by debbugs.gnu.org; 26 Apr 2022 11:36:45 +0000 Received: from localhost ([127.0.0.1]:37289 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJUq-0000kX-F9 for submit@debbugs.gnu.org; Tue, 26 Apr 2022 07:36:44 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJUo-0000j2-D5 for 55124@debbugs.gnu.org; Tue, 26 Apr 2022 07:36:42 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 17F4DA0146 for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:36 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1650972995; x=1652787396; bh=x11rlefoEN6ZkAYQsjy5McXAxk8WAOeDzSA q0su5pLY=; b=QJMLG51qAyXQVwM7zQq6pbUgP67MqDqaQlaBBSM/L0feaFtqtxY M6DoZFrg20g4auKT3QPa/ymi5iEpYCKReLxdKQHhAQL3F/75gdbplYr4kcTMUt5b ob4CpfgWLzdtssgMStJSNQR8NMMaKl2XWlBRlUUAAIgleDj4v9Pmosv4= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id Juvq7thjGK1i for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:35 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:35 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2375.24; Tue, 26 Apr 2022 13:36:34 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <55124@debbugs.gnu.org> Subject: [PATCH 2/2] gnu: Add r-adimpute. Date: Tue, 26 Apr 2022 13:36:23 +0200 Message-ID: <20220426113623.15268-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220426113623.15268-1-madalinionel.patrascu@mdc-berlin.de> References: <20220426113623.15268-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26856.007 X-TM-AS-Result: No-10--1.564900-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyyRKOkRV2jAV1OAfq6beiu9aL yw9otm8JdBLuFwr9gAUiW+eLSpgc6SIqKeoFWulU8+i/lP6Xo8R6OXxdRGLx864avUgr5Bjw1np kix2HfyuiWZEjnmPmoElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RQY+B OHf11ScvcjslNCdyBCOvtBywKSk8XxvL82H0EdeeUxrOgbRwEb2vEDcDbwIXCYkb2N7cmEuYA92 XLoMOWDqRnQfALY3GFkoJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.564900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26856.007 X-TM-SNTS-SMTP: 09B848672C8086D2F0625D0D833EF2723A23DE5825B00AA0F8878FA2658EDFCF2000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 55124 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 07:36:49 2022 Received: (at 55124) by debbugs.gnu.org; 26 Apr 2022 11:36:49 +0000 Received: from localhost ([127.0.0.1]:37292 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJUu-0000l8-UC for submit@debbugs.gnu.org; Tue, 26 Apr 2022 07:36:49 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:35541) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njJUq-0000ja-Ih for 55124@debbugs.gnu.org; Tue, 26 Apr 2022 07:36:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 9A72C160154 for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:38 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1650972997; x=1652787398; bh=CWSJtMT0n0DKE9KshstDIuEWg2+L21LLkt19FKZfaGw=; b=XsE5uxqNxqNL tVfuSMj+O3eoPCQuFk0QhaNln6AvB9DHA7eaX9nBal7I+XEQa5YSpFofTiCBY1LG d5hO+25OXOwo5U4qTjfH9S0uxLipl25cqH4ss5SQ7Z2+2PqMcWFDdkxN+3aEaBAm nTgB5arz+3IofKrHCcR6c4SXDPkri7c= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id SdUDp4sJkl2e for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:37 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <55124@debbugs.gnu.org>; Tue, 26 Apr 2022 13:36:37 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2375.24; Tue, 26 Apr 2022 13:36:34 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <55124@debbugs.gnu.org> Subject: [PATCH 1/2] gnu: Add r-saver. Date: Tue, 26 Apr 2022 13:36:22 +0200 Message-ID: <20220426113623.15268-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26856.007 X-TM-AS-Result: No-10--3.804200-5.000000 X-TMASE-MatchedRID: cSoPLjBYd53/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeMPQRp8uGlvSKQ2 g0AX0DzPb7OzugStl7DuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHEli PkpBtBELCvJ5kI0WAAv9ITYe6vwMlCO3iXlOYXp8qj682BSJncyH8kDR0dp2mUYkZd9+4t2/h06 w0q6p9rIaxlfSrcWmI6EBlBcRddm7Q3sOMB3Fk1OLzNWBegCW2Nfpe10T3IsMLbigRnpKlKXb6c SLExxx2kU6UkIr/V+0Bg4AhdF+KvpNE8+6g09iq2RWLKhzzz0bfu08OsAEThEaX2N5bi+4dhRVp GnM3G+MxpKO4j1304rVxoyzIJc3QHnt0NrCBCg9DAR+FQ0phk9xSR7be7fnTFTs4ljtt094P2K/ +wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.804200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26856.007 X-TM-SNTS-SMTP: 37842D9577755198313E5C12A89D9ADD1C62E714AE0A6296692D6E011DAD0E402000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 55124 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 27 09:52:20 2022 Received: (at 55124-done) by debbugs.gnu.org; 27 Apr 2022 13:52:20 +0000 Received: from localhost ([127.0.0.1]:41654 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nji5c-0006D4-EJ for submit@debbugs.gnu.org; Wed, 27 Apr 2022 09:52:20 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21118) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nji5a-0006Cv-VY for 55124-done@debbugs.gnu.org; Wed, 27 Apr 2022 09:52:19 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1651067535; cv=none; d=zohomail.com; s=zohoarc; b=ifN85IKhX0tS0nPYrHjKSSQCkA6CF/bppQ0HrXXZ87VmwxJTAXFYIhQsHFK0DvqjwOZkoqFB1EN1KuVJ1ooWoMI6THFKpNhrA9t5aUdM8SZGFIrYtb+vORAmNH47hdTTcY5ssEwwL+Ul8OFcAIP/hDt4KnqFda9YQFLNcH8+jX8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1651067535; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=ZFTMG1iElo4TMWu62L2dr3ZyXoZK4n4MBirhOkIy4xA=; b=MpnN2cMT4z4u+0uyiCswEnfciZ1dVJf3pS7oHOVwcWaTUNvS6DdaGgag15gol5ff2I3LScaDbmAlDcLqEovX3Te3R426sdQXTNCLLnOFuS5KwmduGC6zJcdAsDihtYRFRW1Ci7f8wHSv1Fy7lZbUk/hIw7lZALV2vXFTI0i4nqc= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1651067535; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=ZFTMG1iElo4TMWu62L2dr3ZyXoZK4n4MBirhOkIy4xA=; b=KMkfzl1J39s9Q4qMxF4TA/j6hxW6e8MM2zxdE+EX5S0lEBXK4uP3aWyEITejn6Xf ip0DcsY/Jud//ofsoiADt5hr8sy8VLnzfV7geIwsnQKQIg92E/M9937NGu4OvxryMkN /CsX4hg5bmXv1lq9Zy8edWstDZAQ6beAOgPqlePE= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1651067532215582.703256878158; Wed, 27 Apr 2022 06:52:12 -0700 (PDT) User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: 55124-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-adimpute and r-saver Date: Wed, 27 Apr 2022 15:51:30 +0200 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87sfpy4os6.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55124-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks for the patches. I applied them with minor stylistic changes. -- Ricardo From unknown Tue Aug 19 10:01:17 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 26 May 2022 11:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator