From patchwork Mon Dec 5 15:21:51 2022 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: 45053 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 557D227BBEB; Mon, 5 Dec 2022 15:23:45 +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=ham 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 33EBB27BBE9 for ; Mon, 5 Dec 2022 15:23:44 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p2DJD-0004cQ-7u; Mon, 05 Dec 2022 10:23:07 -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 1p2DJ9-0004bl-39 for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:03 -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 1p2DJ8-0000iH-RV for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p2DJ8-0004ME-Kx; Mon, 05 Dec 2022 10:23:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#59835] [PATCH 1/3] gnu: Add r-makecdfenv. References: <7734e3c0299847c9a5c367e2bcf77a6a@mdc-berlin.de> In-Reply-To: <7734e3c0299847c9a5c367e2bcf77a6a@mdc-berlin.de> 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: Mon, 05 Dec 2022 15:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 59835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <59835@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 59835-submit@debbugs.gnu.org id=B59835.167025373416717 (code B ref 59835); Mon, 05 Dec 2022 15:23:02 +0000 Received: (at 59835) by debbugs.gnu.org; 5 Dec 2022 15:22:14 +0000 Received: from localhost ([127.0.0.1]:36662 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIM-0004LT-Fc for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:14 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:60153) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIK-0004L8-Bf for 59835@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:13 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1670253725; x=1672068126; bh=2Puufp+L6+SO27x rQvkoQql0CGX2xuuKIn3N90mhXdY=; b=kUN76sFZF6vythzv9ArNuaPyKMHnhNQ y+6oXdFsadvInkWWbY2P1Pm5wA0+NcZjobAeXUF2YKtYjeDp9ecF/PraVQwH4Qqw VkJO8q1U4UAkeYfQSN86Vi2q0XluiVkSwcPUWNUBqhJHcqKbOwW8WtT0DMZbB5XH Cslq6j46x3ZM= 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 id 538D9A0B25 for <59835@debbugs.gnu.org>; Mon, 5 Dec 2022 16:22:05 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 5 Dec 2022 16:21:51 +0100 Message-ID: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--2.389000-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzrr41gyMH26/v4Y1Mygj090zl xXfg8EXkMpd+A7BXtAA1ArEwC9IavygR7McnOqmXGL//8mlodA0LixrsCJ1jTlCkt7JatNPWeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DGrtcW2vkbkgQ9p72ozF1myE1TN3d73EecSlr 7l4W88yDxUUAO+vgjbtXvKFscnfl4E8He1zaK+jbbPkZG2OgMMW8VxiLyb1RNxSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.389000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 1BDD3B5C8BA3F798CAE97FA0EA8B3DB8009C8F8D5C4C9AEC0477C4FA33ECB0072002: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-makecdfenv): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) base-commit: b2a848d23d37f31496e1ff664f1dcf6abcdcc388 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62c5970b8..7cace3317c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,6 +6010,33 @@ (define-public r-made4 datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an @code{Affymetrix} +@acronym{CDF, chip description file} and creates a hash table environment containing +the location/probe set membership mapping. The other one creates a package that +automatically loads that environment.") + (license license:gpl2+))) + (define-public r-metaneighbor (package (name "r-metaneighbor") From patchwork Mon Dec 5 15:21:52 2022 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: 45054 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 C6BA827BBEC; Mon, 5 Dec 2022 15:23:47 +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=ham 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 171CC27BBE9 for ; Mon, 5 Dec 2022 15:23:47 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p2DJI-0004dZ-7M; Mon, 05 Dec 2022 10:23:12 -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 1p2DJ9-0004bm-6M for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:04 -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 1p2DJ8-0000iG-Uj for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p2DJ8-0004M8-75; Mon, 05 Dec 2022 10:23:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#59835] [PATCH 2/3] gnu: Add r-altcdfenvs. 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: Mon, 05 Dec 2022 15:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 59835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <59835@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 59835-submit@debbugs.gnu.org id=B59835.167025373416710 (code B ref 59835); 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Mon, 5 Dec 2022 16:22:06 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 5 Dec 2022 16:21:52 +0100 Message-ID: <20221205152153.18545-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> References: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--3.419400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCx4SsGg2DQOYulFgQZ3zLO36eM /cGSFB1LMU8NOk/D5DbtCCJ8Cv8fxjzv7niIkhlfG+nS24MzHeQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYUms9rk+YQkcP4CNhPfjljQnjLazFKhX1mRzCofM6icDnRR5 J68wva3EhW1t0FRC7zDF0A9jQ1s1lAVvC16ciJLPpjDNy/updHHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.419400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 257C4DB7866E913F765BC9CD238E247B4FF83AAB5DA767262AF9F7BE5796B6D32002: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-altcdfenvs): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7cace3317c..37b84983c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2492,6 +2492,37 @@ (define-public r-alpine data.") (license license:gpl2+))) +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with @code{Affymetrix GeneChip} short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read @code{R} connections in the @code{FASTA} format +and it can create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") From patchwork Mon Dec 5 15:21:53 2022 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: 45052 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 9FE7127BBEC; Mon, 5 Dec 2022 15:23:43 +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=ham 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 0127227BBE9 for ; Mon, 5 Dec 2022 15:23:42 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p2DJH-0004cW-00; Mon, 05 Dec 2022 10:23:11 -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 1p2DJ9-0004bn-FE for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:04 -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 1p2DJ9-0000iR-7m for guix-patches@gnu.org; Mon, 05 Dec 2022 10:23:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p2DJ9-0004MO-0g; Mon, 05 Dec 2022 10:23:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#59835] [PATCH 3/3] gnu: Add r-harshlight. 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: Mon, 05 Dec 2022 15:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 59835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <59835@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 59835-submit@debbugs.gnu.org id=B59835.167025373516723 (code B ref 59835); Mon, 05 Dec 2022 15:23:02 +0000 Received: (at 59835) by debbugs.gnu.org; 5 Dec 2022 15:22:15 +0000 Received: from localhost ([127.0.0.1]:36664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIM-0004La-Pv for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:15 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:57221) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIL-0004LA-0Q for 59835@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:13 -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=1670253726; x=1672068127; bh=WXzgi3q8bdlg9C6E5G1jBtYDaLoF8/P4ZpGsyxd0UvI=; b=TAHAllevvzBl VCLrQ2Y4+/7u6D89yFbAVfpmsrF6/Zvt5CZALYCQlekCZ6m2xhcjdbfz1Vlw1iWh a9kES1/KDuOVxoo08JxTKvUYwBoH7OsCQ6Eu/Y5rybBcv5VhyI7P+zpGsYxj0ORX HiiiCPP7EangkxGhS6131d4P34WygOo= 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 id D3EE6A0B31 for <59835@debbugs.gnu.org>; Mon, 5 Dec 2022 16:22:06 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 5 Dec 2022 16:21:53 +0100 Message-ID: <20221205152153.18545-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> References: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--0.889200-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90Badv+F8ucSI194/5X9VfCwDhJZ+MB6jvEXjiYP9VKZ993G Y7dNTJ6iI0Ejneva935soi2XrUn/JQYMORuDWAmTfaY87m2dqx8K21zBg2KlfB00/kkeBTwDOct sNf11NFmPrcA4Ba/vN+L7erCxu0i2waTZnVONey9XL378m98lLIQ+dyi4hJiVQmC2dDa5gXh2rC gKe7bbpU5jmVBSXVrQoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.889200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 5E26776C86BADE76E9A3F1CB9BFA5DA15ACE432AA78D5D070E4BBE9FBB3FD0B72002: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-harshlight): 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 37b84983c4..346fccfd3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,6 +5854,33 @@ (define-public r-gseabase Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. @code{Harshlight} marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package replaces +the defected areas with N/As or the median of the values of the same probe. The +new version handles the substitute value as a whole matrix to solve the memory +problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar")