From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 27 07:20:38 2022 Received: (at submit) by debbugs.gnu.org; 27 Apr 2022 11:20:38 +0000 Received: from localhost ([127.0.0.1]:41341 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njfio-0005v0-2u for submit@debbugs.gnu.org; Wed, 27 Apr 2022 07:20:38 -0400 Received: from lists.gnu.org ([209.51.188.17]:39948) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njfim-0005uq-97 for submit@debbugs.gnu.org; Wed, 27 Apr 2022 07:20:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41820) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njfil-00022T-48 for guix-patches@gnu.org; Wed, 27 Apr 2022 07:20:36 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49997) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njfig-00080w-Nd for guix-patches@gnu.org; Wed, 27 Apr 2022 07:20:33 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 1B94E160123 for ; Wed, 27 Apr 2022 13:20:27 +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=1651058426; x=1652872827; bh=7AJWp8HEridv2181Hr8sm0kl26seLUHoO6fmhv512gw=; b=kqPSymQV6sXC xd6jlTn3dAJ1Jul2k9rdhmlp35w3WgAfILbOwqW1wALBASoKnjYbgorgqd8XN4Vc mKWKIWzbznPLv8esHh7heQlZRxvu52NcdtaR1WJvFmqoOdTJNwg0rbPPNbd3nBwc p3x27ZJw9gIMsXDcn2lAe5GXms/lVls= 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 pQFNmgDRW4Ty for ; Wed, 27 Apr 2022 13:20:26 +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 ; Wed, 27 Apr 2022 13:20:25 +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; Wed, 27 Apr 2022 13:20:25 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-agdex. Date: Wed, 27 Apr 2022 13:20:14 +0200 Message-ID: <20220427112014.25581-1-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-14.0.0.3092-9.0.1000-26858.006 X-TM-AS-Result: No-10-2.983500-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJw6 tnDgS/8FRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v95IzfKVROBs87Mvxd5kX6rqbs +nJ/tFJFejJmY5Gw3ZdMqsIeOXZofE6TgnCCr7JqVF2HD8EHNpyN6UuMwMREPsrDwfHQQaK3Jw6 G9NdOWi5KQhRnJRBQnXfrlRZ07b8WCWMXx8ovaCeLzNWBegCW29sZ0UX0EaOILbigRnpKlKTpcQ TtiHDgWf+yF9XYRjrFfkQvdGuR41YRlqTbAvHbKJJ49Ntw2aF9Ml/SsA14gRvQxecuIa2aQkKLB o1PnizLmcaqalUhNaY4MHw8Bw/Mu3yJq1ESN+kMTydv0PB1DgLaNtJpvWmDRSPEWnCfndI6xkkv N/27Ae5RMZUCEHkRt X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.983500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26858.006 X-TM-SNTS-SMTP: 2F0B6129C263738ACA7BC9635740E6ED0F771CED72D9B86E27E81C624A10B9402000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.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-agdex): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67ee6079c6..1de7f83845 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1664,6 +1664,33 @@ (define-public r-adamgui the @code{GFAGpathUi} function.") (license license:gpl2+))) +(define-public r-agdex + (package + (name "r-agdex") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AGDEX" version)) + (sha256 + (base32 + "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64")))) + (properties `((upstream-name . "AGDEX"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-gseabase)) + (home-page "https://bioconductor.org/packages/AGDEX") + (synopsis + "Evaluate agreement of differential expression for cross-species genomics") + (description + "The objective of @code{AGDEX} is to evaluate whether the results of a pair +of two-group differential expression analysis comparisons show a level of +agreement that is greater than expected if the group labels for each two-group +comparison are randomly assigned. The agreement is evaluated for the entire +transcriptome and (optionally) for a collection of pre-defined gene-sets. +Additionally, the procedure performs permutation-based differential expression +and meta analysis at both gene and gene-set levels of the data from each +experiment.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76 -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 27 10:27:48 2022 Received: (at 55145-done) by debbugs.gnu.org; 27 Apr 2022 14:27:48 +0000 Received: from localhost ([127.0.0.1]:43857 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njidv-0001Vv-QW for submit@debbugs.gnu.org; Wed, 27 Apr 2022 10:27:47 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21043) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njidt-0001Vn-Rj for 55145-done@debbugs.gnu.org; Wed, 27 Apr 2022 10:27:46 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1651069664; cv=none; d=zohomail.com; s=zohoarc; b=i2J0l0dbxhbsga226kgPfSODfyWoe4l7cBFCAQlS4/HUGzuOMB+SAoSzIGa9zA1nhbQ8qnrdAuImat7Ow4dd6nRHApLpqJnwJ23TmW+j5/ThB5DpGJspOPNmMMtSkczniGDPz3YqFCYX1lw5VkeIrBkZkqnx6lZ7Zu+jKHFwuHY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1651069664; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=kXuyuVeKb2yAwRpq03gp0SlF7DQG/V6eeRjThWzJFC8=; b=bYNSA/rrZyQ23EarNDEENrV7rIkm4Iz36f5A+Dr4V6OwJM4lRqn3FxqrGJW3XC2ane3cjaX6wU8MpUTc7BIv/ITdihiQMYY0ueB6Ggf4sD3YO9fH7RIyguJwwJ8bHeNxnkD6Ph9UOoeqC4/jpM2Fm9r9+iAlDTkRVHRxpLGq8sI= 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=1651069663; 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=kXuyuVeKb2yAwRpq03gp0SlF7DQG/V6eeRjThWzJFC8=; b=Wap4e3B8RKvdydtEze6282j13zp++/BmO/dyF2S/o4okf/DTzI74MnhSQ4T/htET 2N1slmSz2Lr9B/L/lpwppdWgphC+C3PAxptkObY4C5bVMmYZVFgWz0lyfxwmiRPDM0l cZGVIaxEMaS8bQQI3RRBVysvgETr4E4wflEwb1g0= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1651069662905963.3435589796309; Wed, 27 Apr 2022 07:27:42 -0700 (PDT) References: <20220427112014.25581-1-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#55145] [PATCH] gnu: Add r-agdex. Date: Wed, 27 Apr 2022 16:27:27 +0200 In-reply-to: <20220427112014.25581-1-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: <87bkwm4n4z.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: 55145-done Cc: 55145-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-agdex): New variable. Applied, thanks! --=20 Ricardo From unknown Fri Aug 15 14:45:19 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 11:24:09 +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