From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 23 08:45:37 2022 Received: (at submit) by debbugs.gnu.org; 23 Jun 2022 12:45:37 +0000 Received: from localhost ([127.0.0.1]:37713 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o4MDI-0002Er-Lc for submit@debbugs.gnu.org; Thu, 23 Jun 2022 08:45:36 -0400 Received: from lists.gnu.org ([209.51.188.17]:35432) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o4MDE-0002Al-K4 for submit@debbugs.gnu.org; Thu, 23 Jun 2022 08:45:35 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:57096) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o4MD6-00034e-C8 for guix-patches@gnu.org; Thu, 23 Jun 2022 08:45:26 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34859) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o4MD3-0005Uy-Pg for guix-patches@gnu.org; Thu, 23 Jun 2022 08:45:23 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 412E8160229 for ; Thu, 23 Jun 2022 14:45:14 +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=1655988313; x=1657802714; bh=YAASaC/3MEp1Nj3hEQ77dPaZrifvyLFX7mi41MQe7AU=; b=SFocsJSyPmG4 zZOntGqw/OTAbCBFkN34UP1MEWFEieHZ5CYxWH7DxQ+xn8ru5RUi1pwrkIFTUcM4 ZCams3K3spD5Az4feJcLtI/lH2YNkXcNMHomwzmupTbTVyhGgBc50q3PmEFV+9UP chFOR3YLN2U5vui8cSAxOPvWDsGnI8U= 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 eoKOK4W1xG0z for ; Thu, 23 Jun 2022 14:45:13 +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 ; Thu, 23 Jun 2022 14:45:12 +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 15.1.2507.9; Thu, 23 Jun 2022 14:45:12 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-awst. Date: Thu, 23 Jun 2022 14:44:54 +0200 Message-ID: <20220623124454.28787-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26972.007 X-TM-AS-Result: No-10--1.863300-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxZDdHiTk9OcB8gYJm5tOzEXgY Yd2rut1iGsZX0q3FpiOhAZQXEXXZuTvHzGcGqiIKrm7DrUlmNkIAy6p60ZV62G2i4y8P2xXndB/ CxWTRRu3aDLLDbFMGFn1IP6I52gmj0Cbuoo26p6HUQpG3SJu7PSmCCwemoXu66VvI018icoblLf dRlpwlT54DW3qdl/RyRjHmgLZBbRMISnJrxNJ7Tx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.863300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26972.007 X-TM-SNTS-SMTP: C51C07D9E456C9BB70304566904CD421A160A53E3BD14ED87D51FD3A8B48BFD22002: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-awst): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..fa9c728a44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,32 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-awst + (package + (name "r-awst") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "awst" version)) + (sha256 + (base32 + "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav")))) + (properties `((upstream-name . "awst"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/drisso/awst") + (synopsis "Asymmetric within-sample transformation") + (description + "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that +regularizes RNA-seq read counts and reduces the effect of noise on the +classification of samples. @code{AWST} comprises two main steps: standardization +and smoothing. These steps transform gene expression data to reduce the noise +of the lowly expressed features, which suffer from background effects and low +signal-to-noise ratio, and the influence of the highly expressed features, which +may be the result of amplification bias and other experimental artifacts.") + (license license:expat))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 31 16:37:37 2022 Received: (at 56167-done) by debbugs.gnu.org; 31 Oct 2022 20:37:37 +0000 Received: from localhost ([127.0.0.1]:41950 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbXN-0001Qx-5z for submit@debbugs.gnu.org; Mon, 31 Oct 2022 16:37:37 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21139) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbXK-0001Qo-Lq for 56167-done@debbugs.gnu.org; Mon, 31 Oct 2022 16:37:35 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1667248652; cv=none; d=zohomail.com; s=zohoarc; b=THdw5mQb3cSuYZNcVDRHkK69ntZ0nj3nWWwKeV5cku4XttheuTGuxCPu6YxrI7Wy9LSK2tzrPdAup1K9vpKmP31ae9Gi0XRxi0+VqOSvc9kKwDgCF84u+f1XPKR6w8IE/9LmOQJ0oXkx2WUUvea4N1LhVIIENIBEMKU7ZlLhB6Y= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1667248652; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=Ih/D4MXwL7NmRpAbhcNlqcRzU7kq3tiTi2oywa0mFychEmjuU7QNmizPbSHxixEHrrBSfL7b2cUJzidegmYO5d7iCOBjLL0uZzWYs8fRp+CKBh+qo9cPR1HPrarj0lxMn0fH+uJmc+TWNaw3F80bHk2nRZHITh9gn9TphMB1iCU= 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=1667248652; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=OKV0eaJMELGv/bn87yGPhms7JcCPyTsFl05NhrYH8YWf+v+h8IsDc/J0/UeC7Ivx 68ZGQay3C1Y+EtU40DDfJ1AkkEXi7ilPOS8r6btAf9hLJZ4kQ0WplBuZMOWQnhaStn/ hv9v+y/5oTNZOZUaQhQQ1s2fjDFkgu1d3RUerbRc= Received: from localhost (155-111-142-46.pool.kielnet.net [46.142.111.155]) by mx.zohomail.com with SMTPS id 1667248651621527.8760088352686; Mon, 31 Oct 2022 13:37:31 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56167-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-awst. Date: Mon, 31 Oct 2022 21:37:01 +0100 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: <87v8nzd912.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 56167-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 (-) Applied, thanks! -- Ricardo From unknown Sun Jun 22 11:40:49 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 29 Nov 2022 12:24:11 +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