From patchwork Sat Oct 30 15:55:04 2021 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: 34169 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 4256027BBE1; Sat, 30 Oct 2021 16:56:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id ECDFE27BBE1 for ; Sat, 30 Oct 2021 16:56:15 +0100 (BST) Received: from localhost ([::1]:54572 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mgqiN-0001Pk-1K for patchwork@mira.cbaines.net; Sat, 30 Oct 2021 11:56:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:45352) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001Mn-3E for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46697) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mgqi9-0001Je-Qt for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mgqi9-00086Q-QP for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51513] [PATCH 1/3] gnu: Add r-alluvial. References: <31f4f886465f473f9936beeaba8892ff@mdc-berlin.de> In-Reply-To: <31f4f886465f473f9936beeaba8892ff@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 30 Oct 2021 15:56:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 51513 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <51513@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 51513-submit@debbugs.gnu.org id=B51513.163560933731077 (code B ref 51513); Sat, 30 Oct 2021 15:56:01 +0000 Received: (at 51513) by debbugs.gnu.org; 30 Oct 2021 15:55:37 +0000 Received: from localhost ([127.0.0.1]:58235 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhk-00085A-Bz for submit@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:37 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:57107) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhe-00084m-PM for 51513@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:34 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 7B959A0142; Sat, 30 Oct 2021 17:55:24 +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=1635609324; x=1637423725; bh=d3StqAh8UbRxalby0H/oCY3YNVuMMWLT0RtY36U83x4=; b=ifxQuho0dz8s C8JrK6z7r7xqH0yrtqbbFXuUr2z4fYfCBkbv/R3L06f5EeaTXEnqU3vqgAv6Xhqy prXcnE78mpV9LfqZJ9YrF+HxMhWpLqi5zGVR2BnDFN+lv8gPeSmFFP2KAv8w7Q+x xv2kotibXdqOjZdLg8EiSPX5TATKpMg= 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 dt56hYHVHjAr; Sat, 30 Oct 2021 17:55:24 +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; Sat, 30 Oct 2021 17:55:24 +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 15.1.2308.15; Sat, 30 Oct 2021 17:55:23 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 30 Oct 2021 17:55:04 +0200 Message-ID: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-AS-Result: No-10--0.404200-8.000000 X-TMASE-MatchedRID: v2eT1hosn+AsaaYlMvaOHAPZZctd3P4BLOOFU9c9B/j7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrTT9ZveSPAxX4qCLIu0mtIPj/xqm3b+Mo4ie kOi8xclJvF8Nk3pHf5r1IHVpP7o/N2Uwl4gfKRdLBe89zsi5D0BDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYX6BcwPLz0+ikzfigQEKKKZnipJdGoFdhICYoUv9YqVhwucw J8+r7v5SRWONCVtVqsPgysbpZxsZTvNmIqDEQF58nyIEFzG+UTX7GF+64huyLjmNKuuvgamoYI1 erIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.404200-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-SNTS-SMTP: 673CD435EAA89B06F80F8237FAB3EC7DD6B244CF61051F12472D3CA3867150082000: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-alluvial): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 792ea2a75b..0e79ea0ef2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7070,6 +7070,26 @@ (define-public r-algdesign and within plot factors interact.") (license license:gpl2+))) +(define-public r-alluvial +(package + (name "r-alluvial") + (version "0.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "alluvial" version)) + (sha256 + (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) + (properties `((upstream-name . "alluvial"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mbojan/alluvial") + (synopsis "Creating parallel sets plots (Alluvial Diagrams)") + (description + "The package @code{r-alluvial} creates alluvial diagrams (also known as +parallel sets plots) for multivariate and time series-like data.") + (license license:expat))) + (define-public r-signal (package (name "r-signal") From patchwork Sat Oct 30 15:55:05 2021 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: 34171 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 C5D0A27BBE3; Sat, 30 Oct 2021 16:56:23 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 8566027BBE1 for ; Sat, 30 Oct 2021 16:56:23 +0100 (BST) Received: from localhost ([::1]:55182 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mgqiU-0001qO-KZ for patchwork@mira.cbaines.net; Sat, 30 Oct 2021 11:56:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:45356) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001N0-SW for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46698) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001Jl-7k for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mgqiA-00086a-6H for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51513] [PATCH 2/3] gnu: Add r-stringdb. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 30 Oct 2021 15:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 51513 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <51513@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 51513-submit@debbugs.gnu.org id=B51513.163560934531107 (code B ref 51513); Sat, 30 Oct 2021 15:56:02 +0000 Received: (at 51513) by debbugs.gnu.org; 30 Oct 2021 15:55:45 +0000 Received: from localhost ([127.0.0.1]:58240 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqht-00085e-Am for submit@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:45 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50365) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhr-00085J-RN for 51513@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:44 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 8A78216015F; Sat, 30 Oct 2021 17:55:37 +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= 1635609337; x=1637423738; bh=3ljAQAtQpwNlBIcVBuONrpRsLM7CF9CNvRX KgjnZ70A=; b=dwApVRzTk5nTJGCf7q5ypuF6nAP9XJFl8WatFN/3j/1t4X/t7qg wd4t+YWaNA6oYSq0Vrg/4rapMinl+QS88f8oIxtYGUyKJJnwNq1SOP05jET6pCj0 IgjA9mOQjvVEvlFz2cxNBq2hhGZ+WdGXuVrnt86dNyhZIKqD4pSzmnXA= 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 kZjcBWOu8S1Z; Sat, 30 Oct 2021 17:55:37 +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; Sat, 30 Oct 2021 17:55:37 +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 15.1.2308.15; Sat, 30 Oct 2021 17:55:36 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 30 Oct 2021 17:55:05 +0200 Message-ID: <20211030155506.28269-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 In-Reply-To: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> References: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-AS-Result: No-10--3.071300-8.000000 X-TMASE-MatchedRID: iZqcJIi7cAQsaaYlMvaOHAPZZctd3P4BNwe5zfGEu3r7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qr34b00P59ZxlKhpFNiC3g3hHfiujuTbedxD3 3LnL++e46hh8gmT3PVhZi3foHKexSOWt3LpTk/GVOwmo0laDRbNJMQFCqw2r0cCpx4AmNeLdv2Z iuCbVzY25TfXRL8e4lQJVkw9PTCwiMbvtMrKaNZr09KAokwDFUGmvfI/BKJSxTvZg4AwMmOJ4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyN+E/XGDLHcM8tVOLURmWH/s/52aYm6b+hR55L69TR4dS1Ur mT/WvxEEcNRSx97ZcUxmy8d+XdgqU1smX/HioKcktL3TZ3RYZwYBFqQm66Qna4sJOPPPqqLapBr PywRGWvBBWAh1UbgUTloPhkiH7TGOEw7cMCn7Sw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.071300-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-SNTS-SMTP: 53806B7BD0C8B3B53428007695667916F57838367375650B0FF0B4316CFC9F3B2000: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-stringdb): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..f82427f831 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4337,6 +4337,39 @@ (define-public r-slingshot graph construction.") (license license:artistic2.0))) +(define-public r-stringdb + (package + (name "r-stringdb") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "STRINGdb" version)) + (sha256 + (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm")))) + (properties `((upstream-name . "STRINGdb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gplots" ,r-gplots) + ("r-hash" ,r-hash) + ("r-igraph" ,r-igraph) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcurl" ,r-rcurl) + ("r-sqldf" ,r-sqldf))) + (home-page "https://git.bioconductor.org/packages/STRINGdb") + (synopsis "Searching tool for the retrieval of interacting proteins database") + (description + "The @code{STRINGdb} package provides a R interface to the STRING +protein-protein interactions database. STRING (https://www.string-db.org) is a +database of known and predicted protein-protein interactions. The interactions +include direct (physical) and indirect (functional) associations. Each +interaction is associated with a combined confidence score that integrates the +various evidences.") + (license license:gpl2))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") From patchwork Sat Oct 30 15:55:06 2021 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: 34170 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 9DE2B27BBE1; Sat, 30 Oct 2021 16:56:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 30B3827BBE3 for ; Sat, 30 Oct 2021 16:56:16 +0100 (BST) Received: from localhost ([::1]:54574 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mgqiN-0001Pl-87 for patchwork@mira.cbaines.net; Sat, 30 Oct 2021 11:56:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:45358) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001N1-TR for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46699) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001Jm-IZ for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mgqiA-00086h-Ib for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51513] [PATCH 3/3] gnu: Add r-xina. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 30 Oct 2021 15:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 51513 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <51513@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 51513-submit@debbugs.gnu.org id=B51513.163560935031127 (code B ref 51513); Sat, 30 Oct 2021 15:56:02 +0000 Received: (at 51513) by debbugs.gnu.org; 30 Oct 2021 15:55:50 +0000 Received: from localhost ([127.0.0.1]:58243 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhx-00085y-KP for submit@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:49 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:55881) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhv-00085T-BE for 51513@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:47 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9DAE53000FE; Sat, 30 Oct 2021 17:55:41 +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= 1635609341; x=1637423742; bh=kRKHD/RFu2vioRhUFWKdfOVlpKlo5W59t1V TGnrTtHQ=; b=nwWVr5gfD1r3KQmMZTR9gzN+iMwWuyi1rRbtN07a1Er7cWam1Rz NC+kh+Cr79eVlBQea8wkZOEpevIetDUEBiI008rtt8IUul++q/GjyrKL7oZ4bdfu DXvQgKGAs/65XGeG8ZBiRKGLB1+2hLy88D0A0ZY4XDcFnZM1jSlk+V8k= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 4s598y_FdpzC; Sat, 30 Oct 2021 17:55:41 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS; Sat, 30 Oct 2021 17:55:41 +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 15.1.2308.15; Sat, 30 Oct 2021 17:55:40 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 30 Oct 2021 17:55:06 +0200 Message-ID: <20211030155506.28269-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 In-Reply-To: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> References: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-AS-Result: No-10--2.051700-8.000000 X-TMASE-MatchedRID: 0a+qS+HYqZUsaaYlMvaOHAPZZctd3P4BC//1TMV5chPIFck3f6fvyNN0 iv48FC5C7IvvzMgzLKZM7FV2jxGQluvd6Sh4AjN/nVTWWiNp+v/iTXBy70TaRHOaOgNxEZiuV3U Ws/brCBOp4L5MAnrh2A5Q7W8dBYFUjoR5DwlwBUdX7UpJhGB2Ym3wyFHQiRIJfcujmki2WQLFgy mj9DufconFJ5/U720jPKzpbpsDIY7/dJCaqb+IPN0KiTeJteVB64sVlliWKx8fE8yM4pjsDwtuK BGekqUpOlxBO2IcOBZw6NzqqA359tjB/Q6kjIicYHk8PLD2vOqdxsJWP1Y5ii0eWCYV6MytEC5J Je9+pPXFTmyhZfwo6Hn78542H/LROxqMmHhhomO3ShAi6P5JV4URV9DGzc3pkOCa3xB6S8HmZoJ 42/8sjNUZB2rCwOIS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.051700-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-SNTS-SMTP: 6137070EA08315EDD2961CF1C2A998FD2D284246411F0CDAC0A98BCC6052A54C2000: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-xina): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f82427f831..a232c3fe61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4660,6 +4660,42 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xina + (package + (name "r-xina") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XINA" version)) + (sha256 + (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (properties `((upstream-name . "XINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alluvial" ,r-alluvial) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-mclust" ,r-mclust) + ("r-plyr" ,r-plyr) + ("r-stringdb" ,r-stringdb))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://git.bioconductor.org/packages/XINA") + (synopsis "Identifying proteins that exhibit similar patterns") + (description + "The aim of @code{XINA} is to determine which proteins exhibit similar +patterns within and across experimental conditions, since proteins with +co-abundance patterns may have common molecular functions. @code{XINA} imports +multiple datasets, tags dataset in silico, and combines the data for subsequent +subgrouping into multiple clusters. The result is a single output depicting +the variation across all conditions. @code{XINA}, not only extracts +coabundance profiles within and across experiments, but also incorporates +protein-protein interaction databases and integrative resources such as +@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and +molecular functions, respectively, and produces intuitive graphical outputs.") + (license license:gpl3))) + (define-public r-xvector (package (name "r-xvector")