From unknown Mon Aug 18 08:55:51 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#55121 <55121@debbugs.gnu.org> To: bug#55121 <55121@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-adamgui. Reply-To: bug#55121 <55121@debbugs.gnu.org> Date: Mon, 18 Aug 2025 15:55:51 +0000 retitle 55121 [PATCH] gnu: Add r-adamgui. reassign 55121 guix-patches submitter 55121 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 55121 normal tag 55121 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 06:20:33 2022 Received: (at submit) by debbugs.gnu.org; 26 Apr 2022 10:20:33 +0000 Received: from localhost ([127.0.0.1]:37143 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njIJ6-000874-VL for submit@debbugs.gnu.org; Tue, 26 Apr 2022 06:20:33 -0400 Received: from lists.gnu.org ([209.51.188.17]:51494) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njIJ5-00086x-Kr for submit@debbugs.gnu.org; Tue, 26 Apr 2022 06:20:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:33572) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njIJ5-0005Cl-2e for guix-patches@gnu.org; Tue, 26 Apr 2022 06:20:31 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:45533) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njIJ1-0005N9-5z for guix-patches@gnu.org; Tue, 26 Apr 2022 06:20:30 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id AD0C4A00AE for ; Tue, 26 Apr 2022 12:20:07 +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=1650968406; x=1652782807; bh=Qq7f8KIaL9kvkSPNMMCZF8/IGmQEdvvEmAvzifc57nw=; b=O7j9/z9pi6+f hmHxiBZTZNSefSXlac1FBKXJkLrAnU/bNFXlQv4qYRzJdOPBADoMydUfdJZ/63VJ GVB1NXIBvJbfvsOvfZWl/ilP8bSu0sXAD70O3wf6vizzn9rZyYCQz49huhooIL6a IbPs6mPQM066LkggoKjGl98X1W9ttis= 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 ydurR_bZhyc3 for ; Tue, 26 Apr 2022 12:20:06 +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 ; Tue, 26 Apr 2022 12:20:06 +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 12:20:05 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-adamgui. Date: Tue, 26 Apr 2022 12:19:54 +0200 Message-ID: <20220426101954.8271-1-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-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-14.0.0.3092-9.0.1000-26856.006 X-TM-AS-Result: No-10--6.716600-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6KiJEqUFWRggnGmXufEEYlKY5ZGw7wyeHY87 NwWBxSvjhdgvNa1pTT3f1BeO1K0wqRj+2WVoeCY04hD0Y/Y/a79IEGjPhQBgD64sf0Egj7iqsqx rFSI3/KeO1cUsW4/41ElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuA152LecOHHI4B1x fbMOQ56gxuCBByVKrmKii2ndFRyEA7yRA0+fv41KESZneCvsJ8cvJCgkIGdjA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.716600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26856.006 X-TM-SNTS-SMTP: ED916E809F2F3A7FB6DBAC992ED4A8638F96B617404FC04A998E54FD5C75F72B2000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-adamgui): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa862d736f..484fb2e0a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1616,6 +1616,53 @@ (define-public r-adam functionally associated genes} (GFAG).") (license license:gpl2+))) +(define-public r-adamgui + (package + (name "r-adamgui") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAMgui" version)) + (sha256 + (base32 + "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq")))) + (properties `((upstream-name . "ADAMgui"))) + (build-system r-build-system) + (propagated-inputs (list r-adam + r-colorramps + r-data-table + r-dplyr + r-dt + r-ggplot2 + r-ggpubr + r-ggrepel + r-ggsignif + r-go-db + r-gridextra + r-knitr + r-rcolorbrewer + r-reshape2 + r-shiny + r-shinyjs + r-stringi + r-stringr + r-testthat + r-varhandle)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAMgui/") + (synopsis + "Graphical user interface for gene activity and diversity analysis module") + (description + "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI) for +the @code{ADAM} package. The @code{ADAMgui} package provides 2 shiny-based +applications that allows the user to study the output of the @code{ADAM} +package files through different plots. It's possible, for example, to choose a +specific @dfn{group of functionally associated genes} (GFAG) and observe the +gene expression behavior with the plots created with the @code{GFAGtargetUi} +function. Features such as differential expression and fold change can be +easily seen with aid of the plots made with @code{GFAGpathUi} function.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 30ff557bd7255dddec16f4a032e58f5a88d5e448 -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 17:49:30 2022 Received: (at 55121-done) by debbugs.gnu.org; 26 Apr 2022 21:49:31 +0000 Received: from localhost ([127.0.0.1]:40692 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njT3q-00023U-NC for submit@debbugs.gnu.org; Tue, 26 Apr 2022 17:49:30 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njT3o-00023K-LG for 55121-done@debbugs.gnu.org; Tue, 26 Apr 2022 17:49:29 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1651009766; cv=none; d=zohomail.com; s=zohoarc; b=c4tcqwSEXNVFQNxRzbTBgITsiLcE92G8ppBqxqm2OveeZe9WtX3CTyOYdVLZr8Gkc1uorfW9bZFHTJZFxpPugiw2i/yWR3LPiaoWgVP7oeSxb7oq5XoysBCOwaZzQQMBlsbBOJFhyvQ7Z0f/gX7hERXSaVgnu5VtA9+OON4xtfs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1651009766; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=GxZqgUxne6J05KuT7KRmWW0gxkfQGXs1fZ1C7mWlBGk=; b=aywtKAAW1bUm6QbFnjwuSAvX7zgHZWHCgrZQcsFdQ7WVOuoVjgXr1GCJ8D90p7Uu1S4bHVuqTJ4vzHCoMhbwMYyOVBIY8MM+3cDoMTQ56wmVT76yi7k1XH1GP0jX+9D5zw+DBzgXC0c7SYRxe3O0KuK/U/MFjG22S+9SWansPe8= 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=1651009766; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=GxZqgUxne6J05KuT7KRmWW0gxkfQGXs1fZ1C7mWlBGk=; b=h+LqeTgo2b8c9yXrc3m9CcbZ5P5neWXaEEktSM4O/23hZMHEEyrWxOf/XNmHryBg 6zeg3NozZ6f03GaZo8AMfcza4i+5OrNMk4Nq8s8WoivTKdh1S/F6ECEidG03gQqgDBG bZVrYHWbbAk9WsDTVAccA0XTM9JV9HuT6lwxQ1GI= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1651009764365647.3507546649191; Tue, 26 Apr 2022 14:49:24 -0700 (PDT) References: <20220426101954.8271-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#55121] [PATCH] gnu: Add r-adamgui. Date: Tue, 26 Apr 2022 23:48:55 +0200 In-reply-to: <20220426101954.8271-1-madalinionel.patrascu@mdc-berlin.de> 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: <87wnfb4ise.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55121-done Cc: 55121-done@debbugs.gnu.org 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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioconductor.scm (r-adamgui): New variable. Thanks for the patch! Pushed with minor stylistic changes. --=20 Ricardo From unknown Mon Aug 18 08:55:51 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 25 May 2022 11:24:06 +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