From patchwork Mon Nov 6 11:06:37 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: 55987 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 7CEA927BBEA; Mon, 6 Nov 2023 11:28:24 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 51D2F27BBE2 for ; Mon, 6 Nov 2023 11:28:23 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU2-0000sb-06; Mon, 06 Nov 2023 06:09:30 -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 1qzxTy-0000T2-JI for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTy-0005SK-6w for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUZ-0004LZ-EC; Mon, 06 Nov 2023 06:10:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 01/13] gnu: Add r-breastcancervdx. References: In-Reply-To: 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, 06 Nov 2023 11:10:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926895716548 (code B ref 66966); Mon, 06 Nov 2023 11:10:03 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:17 +0000 Received: from localhost ([127.0.0.1]:38741 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTl-0004IX-Sy for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:17 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51231) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTZ-0004GT-JY for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:10 -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=1699268897; x=1701083298; bh=frQJbmACQpKWqMc rfsvwRH9MmUlXlHhvL+qdgOUuS7A=; b=eUM/FBfIHhb1iC9ocf2chKh5p7QjP6J IRn3a7/mTwGI5eK+0o32ynWdU/mjS8BTWI4nKpo9XnoaWE+i780qM0lK+fyISyft gVAADLJG6aA6y48IYC33SlE/z8XwwZn7qf0PdBOMTvz3rdHNvlhaNhq6VCavx0da mRYiAXQoY0rA= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id F225A300124 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:16 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:16 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:37 +0100 Message-ID: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--5.325400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRuuLH9BII+4qrKs axUiN/ynF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2Klf+Tf0tcxKuLpFTD JQZyN9hKVlm2sCkMyKKFRyFscGEarLKwgB68O1/A== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.325400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 2DD3CAAC52014132E9E94FA259BB6A5707BE139F0D49211B3B28F3827DD931F52000: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-breastcancervdx): New variable. Change-Id: Ia3437ab67a00ce23c61553ff15f940b8a3ee9c8a --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) base-commit: c9361460dece1dbc3d2645ad3e5c79e85a2bf183 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe5ca9fbc7..04a1f2a710 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1463,6 +1463,26 @@ (define-public r-breakpointrdata demonstrate functionalities of the @code{breakpointR} package.") (license license:expat))) +(define-public r-breastcancervdx + (package + (name "r-breastcancervdx") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "breastCancerVDX" version + 'experiment)) + (sha256 + (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0")))) + (properties `((upstream-name . "breastCancerVDX"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/breastCancerVDX") + (synopsis "Gene expression datasets published") + (description + "This package is a collection of gene expression data from a breast cancer +study published in Wang et al. 2005 and Minn et al 2007.") + (license license:artistic2.0))) + (define-public r-celldex (package (name "r-celldex") From patchwork Mon Nov 6 11:06:38 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: 55986 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 7284F27BBEA; Mon, 6 Nov 2023 11:27:53 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 C9DD727BBE2 for ; Mon, 6 Nov 2023 11:27:52 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU2-0000wG-HF; Mon, 06 Nov 2023 06:09:30 -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 1qzxTy-0000X8-Sx for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTy-0005SV-HN for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUZ-0004Lh-QD; Mon, 06 Nov 2023 06:10:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 02/13] gnu: Add r-bags. 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, 06 Nov 2023 11:10:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926895816555 (code B ref 66966); Mon, 06 Nov 2023 11:10:03 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:18 +0000 Received: from localhost ([127.0.0.1]:38744 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTp-0004Ir-H1 for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:17 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51529) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTZ-0004GU-JW for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:10 -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=1699268897; x=1701083298; bh=H3fUpJOTWmZQ1wTwHzIiHkPWPOmS1UK3En9BuWuWRUM=; b=nuGKnBU81CwS CCQhGUWkOW/5HcUJoK7FHIpnZFUUzfv9Rui2mcYRz1+hElaafrvr16FUNKLuA5AA fnxVYzx4Xp2AbDomLMPuocCT3K0IbboywsVzLk5f5jw6LJf8zwzGpl/RrMe6TZ0B Kwt2cThveVg+EGiqNmPQIqiCTiPyg0Q= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 7783130013D for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:17 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:16 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:38 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--1.616600-5.000000 X-TMASE-MatchedRID: /+von0vPuFFRLIODtwQzSQrcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/KqrQ7lLcMnwarNv4Gp08Kiq+GZ9ZHxIhuW77/y896siFzNNPDc6umEyMkq5fGHu2b0G qwJsp9xGLUu/J42Z1x0RANK+qXqVK0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSk6XE E7Yhw4FhPUbt73N46efBaHDy587UgKK8fETp49OyUwbC/lx7naG4HEWoNpNohO4nxMC94oh96WU 23xCL5M74cTiJuk7Uql27A48IN9Wt8iatREjfpDE8nb9DwdQ4C2jbSab1pg0UjxFpwn53SOfhj5 CZkmSyI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.616600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 4ACE8C9C12F06A5D4DDBB99271F73B89B05168D82C55D3540568D8CA54DD47322000: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-bags): New variable. Change-Id: If0c533898a5e05809f23e7e8b52fc3d5fbffc8fb --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 04a1f2a710..47931061af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4036,6 +4036,27 @@ (define-public r-baalchip alleles, a known phenotypical feature of cancer samples.") (license license:artistic2.0))) +(define-public r-bags + (package + (name "r-bags") + (version "2.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BAGS" version)) + (sha256 + (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh")))) + (properties `((upstream-name . "BAGS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-breastcancervdx)) + (home-page "https://bioconductor.org/packages/BAGS") + (synopsis "Bayesian approach for geneset selection") + (description + "This R package is providing functions to perform geneset significance +analysis over simple cross-sectional data between 2 and 5 phenotypes of +interest.") + (license license:artistic2.0))) + (define-public r-basespacer (package (name "r-basespacer") From patchwork Mon Nov 6 11:06:39 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: 55984 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 1667127BBEA; Mon, 6 Nov 2023 11:27:11 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 6B82027BBE2 for ; Mon, 6 Nov 2023 11:27:10 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU5-0001ID-Hg; Mon, 06 Nov 2023 06:09:33 -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 1qzxU0-0000la-U8 for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:29 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxU0-0005UC-J6 for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:28 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUb-0004MQ-QI; Mon, 06 Nov 2023 06:10:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 03/13] gnu: Add r-bsgenome-ecoli-ncbi-20080805. 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, 06 Nov 2023 11:10:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896516597 (code B ref 66966); Mon, 06 Nov 2023 11:10:05 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:25 +0000 Received: from localhost ([127.0.0.1]:38754 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTw-0004Jb-Jf for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:24 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45105) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTZ-0004GW-JS for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:12 -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=1699268897; x=1701083298; bh=D4WwihzSkxAsW2xSC1XAcWRSNkR1HMboB8bwAEDvkOE=; b=LEuel3fUb7Lx +tQhjYnlWg8iU7FPAwnhpPXKRzzsrugREuGIGS5eq0UBk2O/f0QelmWqVvHB2FM7 ZGuVXr9Eh6r99M3FE7zLhqf6n2S/wP9B0/erwcZCxFojNPVrzGejOYPXV/+OZf79 ZWhF5g2xi0pnQOORcxbSo8tH8oOFbeE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id DF894300159 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:17 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:17 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:39 +0100 Message-ID: <39fc6265bb8381c1eb751d96f6c7f06b56710049.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--3.217400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIpb wG9fIuITekMCFQtUEenuNT8xdcEnQwE+dA3RWUSvXke6tLU6lcKFzNNPDc6umOCbuVI7hVbLfEz RZ8UqjkpbJcQH3furVxJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgKIzdZS3ou0WqWZ Ww9A2HeAHddLd4jw6W/oUnwmuVFfhuoMU5ZZojSug+bAabprsQcmY8l99UehNeoO4gBj62Blb35 lOYWJBdPA5yyCesP4xZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.217400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 755796051D734EAD7D5EAD6D1F45ED07E564891A730EF57CEA0E0BE35ACDFBE02000: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-bsgenome-ecoli-ncbi-20080805): New variable. Change-Id: Ic42527fa334be4c23ebe2e19461571d899db77ca --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47931061af..40402f798f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -395,6 +395,28 @@ (define-public r-bsgenome-drerio-ucsc-danrer11 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-ecoli-ncbi-20080805 + (package + (name "r-bsgenome-ecoli-ncbi-20080805") + (version "1.3.1000") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version + 'annotation)) + (sha256 + (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27")))) + (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome)) + (home-page + "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805") + (synopsis "Escherichia coli full genomes") + (description + "Escherichia coli full genomes for several strains as provided by NCBI on +2008/08/05 and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") From patchwork Mon Nov 6 11:06:40 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: 55980 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 9144127BBE9; Mon, 6 Nov 2023 11:21:08 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 9AA2E27BBE2 for ; Mon, 6 Nov 2023 11:21:07 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU0-0000eH-9u; Mon, 06 Nov 2023 06:09:28 -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 1qzxTx-0000IV-Gj for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTx-0005Rp-7U for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUY-0004LA-6o; Mon, 06 Nov 2023 06:10:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 04/13] gnu: Add r-basic4cseq. 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, 06 Nov 2023 11:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926895216497 (code B ref 66966); Mon, 06 Nov 2023 11:10:02 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:12 +0000 Received: from localhost ([127.0.0.1]:38735 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTg-0004HS-Mc for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:11 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49371) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTZ-0004GX-MR for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:07 -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=1699268898; x=1701083299; bh=51GdHKw867/Y00fo/H3USnh/ADfVd/QAZhJU7Aes8BI=; b=Eg4fu7PMMHMG i2UsP7tEHH38Eitp8mndGcaBu9ZKomudhc9ud5nY+n7EABNuGUZo5aooVQpEi/aQ 9OCq+AR4DyAyNJLVdLssNLYlDYVyxLR6iSYozmQWVmC8YHnTDkXux3elIGerpmMy 3z8JBeTkJCvx8azEMr6sGyvNsLy0YYI= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 70641300169 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:18 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:18 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:40 +0100 Message-ID: <5b7e31e4b2e74b0436121dc4e4fbc4e1d59bcec3.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--0.679000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VNnf JrUSEbFDPRxYd0S1w+nuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHja6 jE+UALrWCz1nNrVQH5N4fTYQy9qIcgKExOGpQFYrbKK7hEf18KRDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYWlEtBFnyDyItlBrjK10z9hQCWF4qe0/vgGRJzJT1j++S9Es FqzeNA++AkyUCYyQvTgTt66STXtBb9Ky82tJX/1oNb5KjV6g9PHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.679000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: C39B28CDC8D2E4AB34A205D786DFFDE0799EE4693FA16058335D2087ABDF8F6B2000: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-basic4cseq): New variable. Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3 --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40402f798f..737d1ca2de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22277,6 +22277,37 @@ (define-public r-dir-expiry eliminating obsolete caches generated by old versions of packages.") (license license:gpl3))) +(define-public r-basic4cseq + (package + (name "r-basic4cseq") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Basic4Cseq" version)) + (sha256 + (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4")))) + (properties `((upstream-name . "Basic4Cseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-bsgenome-ecoli-ncbi-20080805 + r-catools + r-genomicalignments + r-genomicranges + r-rcircos)) + (home-page "https://bioconductor.org/packages/Basic4Cseq") + (synopsis "Analyzing 4C-seq data") + (description + "Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and +subsequent visualization of @acronym{4C-seq, circular chromosome conformation +capture sequencing} data. Virtual fragment libraries can be created for any +BSGenome package, and filter functions for both reads and fragments and basic +quality controls are included. Fragment data in the vicinity of the experiment's +viewpoint can be visualized as a coverage plot based on a running median approach +and a multi-scale contact profile.") + (license license:lgpl3))) + (define-public r-basilisk-utils (package (name "r-basilisk-utils") From patchwork Mon Nov 6 11:06:41 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: 55979 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 782A327BBE9; Mon, 6 Nov 2023 11:16:59 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 7F57727BBE2 for ; Mon, 6 Nov 2023 11:16:57 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxTz-0000cF-VK; Mon, 06 Nov 2023 06:09:28 -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 1qzxTx-0000LM-Rm for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTx-0005S0-EM for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUY-0004LI-Ml; Mon, 06 Nov 2023 06:10:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 05/13] gnu: Add r-basics. 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, 06 Nov 2023 11:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926895316515 (code B ref 66966); Mon, 06 Nov 2023 11:10:02 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:13 +0000 Received: from localhost ([127.0.0.1]:38737 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTl-0004I2-0J for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:13 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:59193) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTa-0004GZ-R5 for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:08 -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=1699268899; x=1701083300; bh=CDUvO/++mdS3Ds8w6Y7rX6nfc54DUhic7rSM1RQgyPI=; b=KofDMnTmMtOw InSHow61qAIUoWCpJXC3yeeB8YeANs6cBnNjbzLlXYnqAfke1RzsT5TieE0/vBtN Wci5D54q7gbs4QV4QraSVD4unHmkYf9u1z8syszZ0klrREZVzZd+Arga9sXFzIZp GAtwUFfNc7Oejm+8g44KEKuxbNwoiuE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 08229A014A for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:19 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:18 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:41 +0100 Message-ID: <3efcce969a7ed38c87dcb77b02ab2c551a1709b7.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--7.729800-5.000000 X-TMASE-MatchedRID: kREspPIIG7SOqU9B1spa9grcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/ZNUDHbPZ5K0hMsbW3HSkzCq+GZ9ZHxIhuW77/y896siU29zygMKEf0JZ5MDd4/kUwrj XAJniWteRasqAY6K9mM0YTchqRdqUfww1dQbR7C23AsxGpfAIy50JB6wB6CqmNddXpYgD7Vmm7K ABgpcW3L6RAVv1oriUJOYdsQnSc134xEDDKsmaCQzrPeIO/OIHrixttRG+E/NTvZg4AwMmOJ4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyF82MXkEdQ775QnEgGYiX/ukuXlq67HxXpxzuobGHOTRMtaq 6APnTBULYr8q9nMOXA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.729800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 7376EEADE1C6ECBF4E3CE56BE263835951E7F23C9F5B2E9823CE42ED90FFED452000: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-basics): New variable. Change-Id: I6f0afeeb41f667d780707af65034d5ba978f0d4a --- gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 737d1ca2de..184972afb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22308,6 +22308,56 @@ (define-public r-basic4cseq and a multi-scale contact profile.") (license license:lgpl3))) +(define-public r-basics + (package + (name "r-basics") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BASiCS" version)) + (sha256 + (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8")))) + (properties `((upstream-name . "BASiCS"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biobase + r-biocgenerics + r-biocparallel + r-coda + r-cowplot + r-ggextra + r-ggplot2 + r-hexbin + r-mass + r-matrix + r-matrixstats + r-posterior + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/catavallejos/BASiCS") + (synopsis "Bayesian analysis of single-cell sequencing data") + (description + "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an +integrated Bayesian hierarchical model to perform statistical analyses of +single-cell RNA sequencing datasets in the context of supervised experiments +(where the groups of cells of interest are known a priori. BASiCS performs +built-in data normalisation (global scaling) and technical noise quantification +(based on spike-in genes). BASiCS provides an intuitive detection criterion for +highly (or lowly) variable genes within a single group of cells. Additionally, +BASiCS can compare gene expression patterns between two or more pre-specified +groups of cells.") + (license license:gpl3))) + (define-public r-basilisk-utils (package (name "r-basilisk-utils") From patchwork Mon Nov 6 11:06:42 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: 55978 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 6404627BBEA; Mon, 6 Nov 2023 11:14:17 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 CDC5A27BBE2 for ; Mon, 6 Nov 2023 11:14:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU9-0001f1-0f; Mon, 06 Nov 2023 06:09:37 -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 1qzxU1-0000oq-9t for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:29 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxU0-0005UX-VT for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:28 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUc-0004MY-5p; Mon, 06 Nov 2023 06:10:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 06/13] gnu: Add r-basicstarrseq. 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, 06 Nov 2023 11:10:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896516605 (code B ref 66966); Mon, 06 Nov 2023 11:10:06 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:25 +0000 Received: from localhost ([127.0.0.1]:38756 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTw-0004Je-U7 for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:45885) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTa-0004Gd-TT for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:13 -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=1699268899; x=1701083300; bh=zYzIBCHcTTssxifYlFVIFXQKmxrKiH8spTQauGRGNy4=; b=lUtMXgxa3fy0 oo2aHMskz9JPrGsi36iVzKvW+iaGrybee2EMKnmD+FYw6Lvw3Ff/uhjirgG+XCRy EfrEOSXcfciLqrCxRXeT9CKwhTB++39wwlEJxcewG9+CwK3nbF9n1I/HrM/GIoMe LL5MirjOkrmHf3HyDBT+GddHWzpI5Mk= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 87448A0150 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:19 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:19 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:42 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--6.912400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VNnf JrUSEbFDWVsztmAcPIAarNv4Gp08Kiq+GZ9ZHxIhuW77/y896siFzNNPDc6umOCbuVI7hVbL2Lg EVfggSlh9VK5Cn+Wq2GHWCzyI6Edo4zsKUywVOSbEOJqSsn5KmYaJp9G8IFZph5L4VA9wKIzQ+f Ytbxda88X4oKkYTfsImyiLZetSf8nyb6HMFK1qe3YJEUfDojP/wrbXMGDYqV8LH2qjGZLbHREyp KEfQOwrO3LAunBmTXo07cgPTcaOlIs2uD2sq01E X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.912400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 37C1985A334EFFD215585EB2BFD4CE2B0113CDDC60794BEBA850F95E97C0B77F2000: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-basicstarrseq): New variable. Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604 --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 184972afb5..986227ec38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22358,6 +22358,39 @@ (define-public r-basics groups of cells.") (license license:gpl3))) +(define-public r-basicstarrseq + (package + (name "r-basicstarrseq") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BasicSTARRseq" version)) + (sha256 + (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa")))) + (properties `((upstream-name . "BasicSTARRseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BasicSTARRseq") + (synopsis "Basic peak calling on STARR-seq data") + (description + "This package implements a method that aims to identify enhancers on large +scale. The STARR-seq data consists of two sequencing datasets of the same targets +in a specifc genome. The input sequences show which regions where tested for +enhancers. Significant enriched peaks i.e. a lot more sequences in one region +than in the input where enhancers in the genomic DNA are, can be identified. So +the approach pursued is to call peak every region in which there is a lot more +(significant in a binomial model) STARR-seq signal than input signal and propose +an enhancer at that very same position. Enhancers then are called weak or strong +dependent of there degree of enrichment in comparison to input.") + (license license:lgpl3))) + (define-public r-basilisk-utils (package (name "r-basilisk-utils") From patchwork Mon Nov 6 11:06:43 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: 55990 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 6F1B027BBEA; Mon, 6 Nov 2023 11:34:51 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 A54C627BBE2 for ; Mon, 6 Nov 2023 11:34:50 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU1-0000m4-64; Mon, 06 Nov 2023 06:09:29 -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 1qzxTy-0000Pl-7Z for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTx-0005SA-QZ for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUZ-0004LR-2U; Mon, 06 Nov 2023 06:10:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 07/13] gnu: Add r-bayesknockdown. 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, 06 Nov 2023 11:10:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926895416528 (code B ref 66966); Mon, 06 Nov 2023 11:10:03 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:14 +0000 Received: from localhost ([127.0.0.1]:38739 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTl-0004IK-DQ for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:13 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:55599) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTb-0004Ge-80 for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:08 -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=1699268900; x=1701083301; bh=05GSNLxKRmHt/Q1TGNM6h3NVSYb4OF8hhjtcvjWPlgs=; b=ovl/HLs2VjV0 PyTdUTondBOGslhzOz6yWRlHJc4t6utxqR71EAXfYilC5P7KXfFeGKWEnHWLsuqp 8H3p+EkwA90OiIoa3MZPwWpX3WFq/ivSVi5BQog9thWs531QkkFrqa2g0T7Mg67y oMVedKRgLrz+PDPvfU/y8wO5kiHgKJ4= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 11E9AA015C for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:20 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:19 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:43 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--5.136600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRm1/OiWPM9c7tgV GX4yLLNbD/uHRcacpeKI1Q85Nw6wpG3Jt29YAwfDdCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgW8Z9kpD/pnfb/AwNMnz4zxJLD+/KY3n+qXGv7y7WL/wmHV2pk/r4Ntw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.136600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: A98C9F628791D22BA2BB8F0F7D2B689868DFCCC6B673212B13FF2D23FA6F8D5E2000: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-bayesknockdown): New variable. Change-Id: Icceffc04071efaa8a8b79144005fa7745abc7e1a --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 986227ec38..12d9e1b077 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22441,6 +22441,30 @@ (define-public r-basilisk Python environments in a single R session.") (license license:gpl3))) +(define-public r-bayesknockdown + (package + (name "r-bayesknockdown") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesKnockdown" version)) + (sha256 + (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8")))) + (properties `((upstream-name . "BayesKnockdown"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/BayesKnockdown") + (synopsis "Posterior probabilities for edges from knockdown data") + (description + "This package provides a simple, fast Bayesian method for computing posterior +probabilities for relationships between a single predictor variable and multiple +potential outcome variables, incorporating prior probabilities of relationships. +In the context of knockdown experiments, the predictor variable is the +knocked-down gene, while the other genes are potential targets. Can also be +used for differential expression/2-class data.") + (license license:gpl3))) + (define-public r-biocthis (package (name "r-biocthis") From patchwork Mon Nov 6 11:06:44 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: 55981 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 4ACD627BBEA; Mon, 6 Nov 2023 11:24:04 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 1C0FC27BBE2 for ; Mon, 6 Nov 2023 11:24:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU5-0001JX-Qd; Mon, 06 Nov 2023 06:09:33 -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 1qzxU1-0000s3-Nw for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:29 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxU1-0005Ut-CK for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:29 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUc-0004Mj-KL; Mon, 06 Nov 2023 06:10:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 08/13] gnu: Add r-rcppdist. 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, 06 Nov 2023 11:10:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896516612 (code B ref 66966); Mon, 06 Nov 2023 11:10:06 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:25 +0000 Received: from localhost ([127.0.0.1]:38758 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTx-0004Jm-9s for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51913) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTd-0004Gg-Lz for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:14 -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=1699268900; x=1701083301; bh=rhFq7PZPyRSEGHHhDIxLsOnY93q3RMCS6/TJ0mTO2xc=; b=FUKDZnbr6e/N tRZPKq5+iun1ieU0FCzCj7y1kzM4Bk+oR2yh/Azk67xf2JuQckB3qS0TNb9+5Uhl a64GUzJ0Y/srmicGUvG/VyrmGgIO5Mh9omhSKHnogs4wXMf/NyqXg5v7pUSr2YcR 96ofeqnQY30TA2FhH2mpwrdAIoMqnlE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id C66E6160146 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:20 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:20 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:44 +0100 Message-ID: <0dcafe2494c39d2d44971cf081917548de08552f.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--6.884900-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VL6p xbTOjavy84lM8MUZ3FnuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeH+fA vi4UZBM/2oEyvZrhU9izgLIMbM3DNQLBrHsp/dPM4nl8G25DNkq4sbbURvhPzIpz++XQI8PGeAi CmPx4NwGmRqNBHmBveVDC1CbuJXmMqtq5d3cxkNZd/mwLf2BVUqpikrgfXiNCAgylnn4EYLug8i Vy7g/TGsg78o6VbsdlfCOKFKuVYGg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.884900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: BA7081AB3CA2F87B93AFBBDC09AE05561162BA8ABEB1F3589BF8A8BBE5366B692000: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/cran.scm (r-rcppdist): New variable. Change-Id: Iaa99d2b9c63f6803979ec74f471d2d60a2bf0635 --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 30f28f6adc..18dd82fd03 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6132,6 +6132,30 @@ (define-public r-rcppde performs global optimization by differential evolution.") (license license:gpl2+))) +(define-public r-rcppdist + (package + (name "r-rcppdist") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppDist" version)) + (sha256 + (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x")))) + (properties `((upstream-name . "RcppDist"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/duckmayr/RcppDist") + (synopsis "Integration of additional probability distributions") + (description + "RcppDist provides a header-only C++ library with functions for additional +statistical distributions that can be called from C++ when writing code using +Rcpp or RcppArmadillo. Functions are available that return a @code{NumericVector} +as well as doubles, and for multivariate or matrix distributions, Armadillo +vectors and matrices.") + (license license:gpl2+))) + (define-public r-rcppml (package (name "r-rcppml") From patchwork Mon Nov 6 11:06:45 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: 55983 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 16D8E27BBEA; Mon, 6 Nov 2023 11:24:55 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 4F75227BBE2 for ; Mon, 6 Nov 2023 11:24:53 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU5-0001D4-2B; Mon, 06 Nov 2023 06:09:33 -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 1qzxU0-0000j7-IG for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:28 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxU0-0005Tx-6y for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:28 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUb-0004MG-EL; Mon, 06 Nov 2023 06:10:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 09/13] gnu: Add r-bayesspace. 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, 06 Nov 2023 11:10:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896416589 (code B ref 66966); Mon, 06 Nov 2023 11:10:05 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:24 +0000 Received: from localhost ([127.0.0.1]:38752 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTw-0004JQ-1t for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:24 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44119) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTc-0004Gi-PG for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:12 -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=1699268901; x=1701083302; bh=cibABNdqXPlKApeGgdeYYqf7cmG/CQaDj0yjf4pMnfo=; b=lE+otUb9nIXp 4aTkhhrpcVHcQWPR3OVxFjfOsHAvqQhH/IHO3QSsu0hNx+oVmevmlLVBn4Btjn8Z SnF+T8OBxDOTKa3qgsKxln7Nc49Njt5G+ZWfg8Tf5FSYXd3YXMRn3488/9cfJttX vIduvWQD2+DIbcMaHtNcBVs5IVKOc+I= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8C5E530016F for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:21 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:20 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:45 +0100 Message-ID: <65aee48b6b97ac04afc0ce82770eba08177d9f2f.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--5.279400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCba+BtDYmoqPpbuNT8xdcEnQwE+dA3RWUSvnMRCqQzD5eeFzNNPDc6umOCbuVI7hVbLe4t 0yVpGKXl7MSP7SLpuGAr/hpwkKZyY9GKMj6bPDPRvTnqYKYXTRhDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7IhKJwzCNgn/Ix3Icp6zuW/DSSPzCyykoAmhvoAOTjhCck9+wYbSFlglzW lI5hfAH X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.279400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 4150BF2D6396179609050E708F11F322D2934D3405FA163B0795AC7E4A7EF2F12000: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-bayesspace): New variable. Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12d9e1b077..11ed82bc58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22465,6 +22465,53 @@ (define-public r-bayesknockdown used for differential expression/2-class data.") (license license:gpl3))) +(define-public r-bayesspace + (package + (name "r-bayesspace") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesSpace" version)) + (sha256 + (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105")))) + (properties `((upstream-name . "BayesSpace"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocfilecache + r-biocsingular + r-coda + r-dirichletreg + r-ggplot2 + r-matrix + r-mclust + r-purrr + r-rcpp + r-rcpparmadillo + r-rcppdist + r-rcppprogress + r-rcurl + r-rhdf5 + r-s4vectors + r-scales + r-scater + r-scran + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://www.ezstatconsulting.com/BayesSpace/") + (synopsis "Clustering and resolution enhancement of spatial transcriptomes") + (description + "This package provides tools for clustering and enhancing the resolution of +spatial gene expression experiments. BayesSpace clusters a low-dimensional +representation of the gene expression matrix, incorporating a spatial prior to +encourage neighboring spots to cluster together. The method can enhance the +resolution of the low-dimensional representation into \"sub-spots\", for which +features such as gene expression or cell type composition can be imputed.") + (license license:expat))) + (define-public r-biocthis (package (name "r-biocthis") From patchwork Mon Nov 6 11:06:46 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: 55991 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 18CA327BBEA; Mon, 6 Nov 2023 11:36:46 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 6AC5127BBE2 for ; Mon, 6 Nov 2023 11:36:45 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU1-0000sB-US; Mon, 06 Nov 2023 06:09:30 -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 1qzxTz-0000Ze-Br for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:27 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTy-0005Sn-Uf for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:26 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUa-0004Lq-6G; Mon, 06 Nov 2023 06:10:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 10/13] gnu: Add r-bb. 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, 06 Nov 2023 11:10:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896316567 (code B ref 66966); Mon, 06 Nov 2023 11:10:04 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:23 +0000 Received: from localhost ([127.0.0.1]:38746 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTp-0004Iy-UP for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:23 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36821) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTd-0004Gl-8b for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:10 -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=1699268902; x=1701083303; bh=pAwYm8lAr2Rp9M7vaYqip9mutalxVX4YQeoRbh3aEWQ=; b=KnPlJ90uTm/x uyh8HDH3EFKYODcGk1j15E4tvK/96fmo9NBnjAogURChR4iksREN1agifPXv+eRn RhWPWdWw21Z+gOffNomgJMaKIkceO1es8UUiPdUf5k7/Efi1gKNoE4JTc3lsAQNp r1zlzV9j3TU5DR+TRxqF/0Olb20V2Wg= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1D56CA0164 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:22 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:21 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:46 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--1.581400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v995kRsYEJuFhtD2wLcqqOw2Lg EVfggSlgIZt1/68fFfncoyE7Gc9e7nesCJvzd5qWrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGFIrx2nJK7uZH68ikMogtfDOudUCXg0t5izn/vgIOzQS/e06Ze4gf+Xcdnz 9F783MJ3A47R4GQpNQm5OlAJ6inRy0PqfVJR/SFx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.581400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 35AE2DFD5E8BB37D6FF1052F40F28955BC88B6B491B0C27F028206D67A72A0D72000: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/cran.scm (r-bb): New variable. Change-Id: Ia1f4ca93fd91d7da5c105b70683f7ecb913079a0 --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 18dd82fd03..20d86487f0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6266,6 +6266,27 @@ (define-public r-rcppxptrutils components.") (license license:expat))) +(define-public r-bb + (package + (name "r-bb") + (version "2019.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "BB" version)) + (sha256 + (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04")))) + (properties `((upstream-name . "BB"))) + (build-system r-build-system) + (propagated-inputs (list r-quadprog)) + (home-page "https://publichealth.jhu.edu/") + (synopsis "Solving and optimizing large-scale nonlinear systems") + (description + "This package implements Barzilai-Borwein spectral methods for solving +nonlinear system of equations, and for optimizing nonlinear objective functions +subject to simple constraints.") + (license license:gpl3))) + (define-public r-bindr (package (name "r-bindr") From patchwork Mon Nov 6 11:06:47 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: 55989 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 9766A27BBEA; Mon, 6 Nov 2023 11:33:07 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 EA1E827BBE2 for ; Mon, 6 Nov 2023 11:33:06 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU2-0000vb-Do; Mon, 06 Nov 2023 06:09:30 -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 1qzxTz-0000cC-RA for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:27 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTz-0005TG-Cq for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:27 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUa-0004Ly-JU; Mon, 06 Nov 2023 06:10:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 11/13] gnu: Add r-baynorm. 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, 06 Nov 2023 11:10:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896316575 (code B ref 66966); Mon, 06 Nov 2023 11:10:04 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:23 +0000 Received: from localhost ([127.0.0.1]:38748 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTv-0004JF-9e for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:23 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:40171) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTe-0004Gn-Su for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:11 -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=1699268902; x=1701083303; bh=hhz5zaQSQeditYNRaXBbDFk0OT7djd2A4PawLv7jQdk=; b=LjRkuDA4revh x2CjvthdlBeN4RnWY//7ejUeRw34XFb2LPzc3wYk6zJhP82vPUeRhs2MxQBmTdyi 8g6IZJigMSX7GL0qwa/qeG2nYG1kkNeq2T4wJEFxijoPsRUlnKjjuPrTH6m4Dk+z +h/3AICKQ/e8D6Cz4Kd41sorqWqCTTo= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 807C6A016C for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:22 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:22 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:47 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--2.296400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8xLxDYO3UlDDsyZ/vGp8aUqpc 0qSXG1rfjntNT3A3P5wGDTGLhNrAfuJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGjmU93iMSDFGeAeeT0+IfgvmFWK3Glg2pUE+eNWYniPUbknnlZSKpfx1WTTnfqzl88ThS BDtEcdW0JIru4xMINGoB/NJsfDNZLvXupsC9+EvtOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.296400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 6D33A14A9DB2D7E8AEE92F041A37E21D2F1F2EE45614B9DBCB90B2058E4051052000: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-baynorm): New variable. Change-Id: I83e82d3d0362874918f423ab01f038c74f3eb265 --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11ed82bc58..a8fa9d7af4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22512,6 +22512,44 @@ (define-public r-bayesspace features such as gene expression or cell type composition can be imputed.") (license license:expat))) +(define-public r-baynorm + (package + (name "r-baynorm") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bayNorm" version)) + (sha256 + (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq")))) + (properties `((upstream-name . "bayNorm"))) + (build-system r-build-system) + (propagated-inputs + (list r-bb + r-biocparallel + r-dosnow + r-fitdistrplus + r-foreach + r-iterators + r-locfit + r-mass + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/WT215/bayNorm") + (synopsis "Single-cell RNA sequencing data normalization") + (description + "The bayNorm package is used for normalizing single-cell RNA-seq data. The +main function is bayNorm, which is a wrapper function for gene specific prior +parameter estimation and normalization. The input is a matrix of scRNA-seq data +with rows different genes and coloums different cells. The output is either +point estimates from posterior (2D array) or samples from posterior (3D array).") + (license license:gpl2+))) + (define-public r-biocthis (package (name "r-biocthis") From patchwork Mon Nov 6 11:06:48 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: 55985 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 6265327BBE9; Mon, 6 Nov 2023 11:27:45 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 095C427BBE2 for ; Mon, 6 Nov 2023 11:27:44 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU4-00016I-0f; Mon, 06 Nov 2023 06:09:32 -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 1qzxU2-0000uF-4v for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:30 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxU1-0005VM-RC for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:29 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUd-0004Mr-3J; Mon, 06 Nov 2023 06:10:07 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 12/13] gnu: Add r-bbcanalyzer. 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, 06 Nov 2023 11:10:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896616618 (code B ref 66966); Mon, 06 Nov 2023 11:10:07 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:26 +0000 Received: from localhost ([127.0.0.1]:38760 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTx-0004Jt-L7 for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:25 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:32929) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTl-0004HR-R8 for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:14 -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=1699268903; x=1701083304; bh=gbpaNSxCjUPdl4k2OkutW96QoVADUjzunNvzRWjTD00=; b=b7lVk3GZvoGh j2FJQGt+B3O8ubzgYsnMHgBHATvppn9RPPCBjxsIle5VjgcmRq8Bo/He32n+CUbb dlM1hPZ+lu8YfhqCZBuxtBGGHi6Ybvr4FPHyHkqdgM9QWLKD+BjqNTivQ8ai8Kro +2T5inKGUxNRXs0VtWh+JQ3+Eo5lgqc= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id E8EB8A0174 for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:22 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:22 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:48 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--4.358400-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIpb wG9fIuITg5ortHq/YwzuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIG90ib0DF+dekYd nzk6dz7ZJ0E97gFtA7vg6HAfVSMztRY1tl9vG/AZpTt57XuqMc7gR9C4UwCZzU72YOAMDJjieAi CmPx4NwGmRqNBHmBvepuP9zg477pEqtq5d3cxkNRqXnrxrKCOXC3Y6LKU69sa4g9fZ8yqiVjoCE 5u7n8bKZ/4k0C9c/3Wv6QeM6WQuoZZfiZmBIt6G/XhfwDztFZwhPvjE2hs/a1uaKj27vbj1DUEk BTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.358400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 2CD99D41E503FFD99C4D9D92D45F2A94729BACAB6DFCD87C7CD2893B6447A1F52000: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-bbcanalyzer): New variable. Change-Id: Icd3c77c9522d73638ddb0934ad332ddb7b947a8e --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8fa9d7af4..384bb7cbdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22550,6 +22550,36 @@ (define-public r-baynorm point estimates from posterior (2D array) or samples from posterior (3D array).") (license license:gpl2+))) +(define-public r-bbcanalyzer + (package + (name "r-bbcanalyzer") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BBCAnalyzer" version)) + (sha256 + (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1")))) + (properties `((upstream-name . "BBCAnalyzer"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomicranges + r-iranges + r-rsamtools + r-summarizedexperiment + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BBCAnalyzer") + (synopsis "Visualizing base counts") + (description + "BBCAnalyzer is a package for visualizing the relative or absolute number +of bases, deletions and insertions at defined positions in sequence alignment +data available as bam files in comparison to the reference bases. Markers for +the relative base frequencies, the mean quality of the detected bases, known +mutations or polymorphisms and variants called in the data may additionally be +included in the plots.") + (license license:lgpl3))) + (define-public r-biocthis (package (name "r-biocthis") From patchwork Mon Nov 6 11:06:49 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: 55982 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 EDDC327BBE2; Mon, 6 Nov 2023 11:24:39 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 555C327BBE2 for ; Mon, 6 Nov 2023 11:24:39 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzxU5-0001DF-4J; Mon, 06 Nov 2023 06:09:33 -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 1qzxU0-0000g7-8U for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:28 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qzxTz-0005Tj-SA for guix-patches@gnu.org; Mon, 06 Nov 2023 06:09:27 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzxUb-0004M6-2Z; Mon, 06 Nov 2023 06:10:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66966] [PATCH 13/13] gnu: Add r-bcrank. 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, 06 Nov 2023 11:10:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66966 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66966@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66966-submit@debbugs.gnu.org id=B66966.169926896416583 (code B ref 66966); Mon, 06 Nov 2023 11:10:05 +0000 Received: (at 66966) by debbugs.gnu.org; 6 Nov 2023 11:09:24 +0000 Received: from localhost ([127.0.0.1]:38750 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTv-0004JI-JR for submit@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:24 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43885) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzxTf-0004Gw-4B for 66966@debbugs.gnu.org; Mon, 06 Nov 2023 06:09:11 -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=1699268903; x=1701083304; bh=4nsDQAYLJMO0xik0RkfIxoUO3ipreRiNxz57x3QpePY=; b=lWCPui+p+TOV fwbHAIHP8M9utgpM3W1stFlzstc9GMmKVS4ThWlWEyhB6h9gQDNka7agIUStzHlD JYATapQgw1gsCvz0atjRq+hif8e7FwP/R3+t6cjhAKI2kUobzSqKQIwwLKPTg640 +iyDc8jNlCq2ii+qJ7hyWBGjH+m1Ekw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 95A5616014E for <66966@debbugs.gnu.org>; Mon, 6 Nov 2023 12:08:23 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 6 Nov 2023 12:08:23 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 6 Nov 2023 12:06:49 +0100 Message-ID: <2a5f4950bdea0436db684fe25aab7e7d2c7890c3.1699268809.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> References: <302230715db60dbcab23676e1c67c53a567884e2.1699268809.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-AS-Result: No-10--6.021600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8V6Llg/k2+wrM+ei5Ef8HKqbs +nJ/tFJFLdouwhkFzvsBSF5SyieX8uJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr13fgKwz+1Dc6JusHeGbRUoQQ0tPvVJ9TjF/WnDr8NPg1gIq0zp26oDQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.021600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27980.005 X-TM-SNTS-SMTP: 2D2365CBCE21E3C6FD16A8542747F63881972378333ACD1682FBA1230B9010882000: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-bcrank): New variable. Change-Id: Id43ae3b7f6eff54e1180b489c90fc72176751f9f --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 384bb7cbdf..a3ce78071b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22580,6 +22580,26 @@ (define-public r-bbcanalyzer included in the plots.") (license license:lgpl3))) +(define-public r-bcrank + (package + (name "r-bcrank") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BCRANK" version)) + (sha256 + (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9")))) + (properties `((upstream-name . "BCRANK"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings)) + (home-page "https://bioconductor.org/packages/BCRANK") + (synopsis "Predicting binding site consensus from ranked DNA sequences") + (description + "This package provides functions and classes for de novo prediction of +transcription factor binding consensus by heuristic search.") + (license license:gpl2))) + (define-public r-biocthis (package (name "r-biocthis")