From patchwork Tue Apr 26 11:36:22 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 38903 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0A78627BBEA; Tue, 26 Apr 2022 12:37:40 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id AA44727BBE9 for ; Tue, 26 Apr 2022 12:37:39 +0100 (BST) Received: from localhost ([::1]:52482 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njJVi-00079Z-Lb for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 07:37:38 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51424) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njJVA-0006wE-Ch for guix-patches@gnu.org; Tue, 26 Apr 2022 07:37:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43397) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njJVA-0002Um-2s for guix-patches@gnu.org; Tue, 26 Apr 2022 07:37:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njJV9-0000no-S5; Tue, 26 Apr 2022 07:37:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55124] [PATCH 1/2] gnu: Add r-saver. References: <7d2f41e893ea40a98618c962d4f02ca5@mdc-berlin.de> In-Reply-To: <7d2f41e893ea40a98618c962d4f02ca5@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 11:37:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55124 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <55124@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 55124-submit@debbugs.gnu.org id=B55124.16509730092926 (code B ref 55124); Tue, 26 Apr 2022 11:37:03 +0000 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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-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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-saver): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) base-commit: 30ff557bd7255dddec16f4a032e58f5a88d5e448 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 From patchwork Tue Apr 26 11:36:23 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 38902 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id AC60D27BBEA; Tue, 26 Apr 2022 12:37:23 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 381A527BBE9 for ; Tue, 26 Apr 2022 12:37:23 +0100 (BST) Received: from localhost ([::1]:52230 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njJVS-0006wM-C7 for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 07:37:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51422) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njJV9-0006w5-MQ for guix-patches@gnu.org; Tue, 26 Apr 2022 07:37:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43395) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njJV9-0002Ue-2I for guix-patches@gnu.org; Tue, 26 Apr 2022 07:37:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njJV8-0000nY-Vg for guix-patches@gnu.org; Tue, 26 Apr 2022 07:37:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55124] [PATCH 2/2] gnu: Add r-adimpute. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 11:37:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55124 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <55124@debbugs.gnu.org> Received: via spool by 55124-submit@debbugs.gnu.org id=B55124.16509730052895 (code B ref 55124); Tue, 26 Apr 2022 11:37:02 +0000 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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")