From patchwork Thu Feb 2 02:26:53 2023 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: 46577 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 1B0BC27BBEB; Thu, 2 Feb 2023 02:29:01 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 7B74327BBE9 for ; Thu, 2 Feb 2023 02:28:58 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNPKd-0001DY-L4; Wed, 01 Feb 2023 21:28:11 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pNPKW-0001Ap-Hr for guix-patches@gnu.org; Wed, 01 Feb 2023 21:28:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pNPKV-0005Aq-HB for guix-patches@gnu.org; Wed, 01 Feb 2023 21:28:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNPKV-0002Ph-DB; Wed, 01 Feb 2023 21:28:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61220] [PATCH 06/10] gnu: Add r-tilingarray. 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: Thu, 02 Feb 2023 02:28:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61220 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61220@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 61220-submit@debbugs.gnu.org id=B61220.16753048449128 (code B ref 61220); Thu, 02 Feb 2023 02:28:03 +0000 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:24 +0000 Received: from localhost ([127.0.0.1]:60207 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJs-0002N8-Fv for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:24 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43575) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJp-0002M7-Mr for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:22 -0500 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; s=mdc; t=1675304835; x=1677119236; bh=x7Rj4BYlUECBsOz70fYLg6yWGgfDVCQV3ZZ8lKM9W3A=; b=LLPqb3w8v8Rg KCp1G7gQH/U/w4CNffxRQzhsWM3Li0g1/dn4prwGCxvQh74rVmkBfRhYXGpoKCSI NIAY2CjICFW+1GwPJ6YE0ATN7t1up4oXFh/RREhjUBkqtX54avcOgPbN7rn2WzvU O1ekZYWCSVaKiR1tFDLgljpxVGXVNGc= 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 id 9154C16065F for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:15 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 2 Feb 2023 03:26:53 +0100 Message-ID: <20230202022657.67003-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--2.269400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEA/v U1gmU80CRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9RMEg8Dnr1Idx+VvL9O1ekqbs +nJ/tFJG0SiDAofBoqSN0tVE7uH9szNgzYXdSUcZtN2GsBybzwoH9xUWW6Ss7//6LNRWr/sZ3M/ 6StC/mW5ST9wVeygStElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RXv6l X5VNikhH8BAZ8ekpzbbrzJkbSyyQUHG1Xeby7FiV0RXAp+XvmUNKdIYtXp3n4KlgLrKWH76i4R+ iqqc8XMMRrDp03LKnlkoJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.269400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 7268F267B0D8A78EDA56157011708AAE478692E7596318A273C680FF288B661A2002: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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-tilingarray): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3339c751cb..f692114754 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14960,6 +14960,46 @@ (define-public r-wavcluster procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) +(define-public r-tilingarray + (package + (name "r-tilingarray") + (version "1.76.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tilingArray" version)) + (sha256 + (base32 + "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) + (properties `((upstream-name . "tilingArray"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-genefilter + r-pixmap + r-rcolorbrewer + r-strucchange + r-vsn)) + (home-page "https://bioconductor.org/packages/tilingArray") + (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays") + (description + "The package provides functionality that can be useful for the analysis of +the high-density tiling microarray data (such as from Affymetrix genechips) or for +measuring the transcript abundance and the architecture. The main functionalities +of the package are: +@enumerate +@item the class segmentation for representing partitionings of a linear series of +data; +@item the function segment for fitting piecewise constant models using a dynamic +programming algorithm that is both fast and exact; +@item the function confint for calculating confidence intervals using the strucchange +package; +@item the function plotAlongChrom for generating pretty plots; +@item the function normalizeByReference for probe-sequence dependent response +adjustment from a (set of) reference hybridizations. +@end enumerate") + (license license:artistic2.0))) + (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment")