From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id UN/RDRkPaGIg8QAAbAwnHQ (envelope-from ) for ; Tue, 26 Apr 2022 17:26:17 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id ENjNDRkPaGJEZgAAauVa8A (envelope-from ) for ; Tue, 26 Apr 2022 17:26:17 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id A54D1264CA for ; Tue, 26 Apr 2022 17:26:16 +0200 (CEST) Received: from localhost ([::1]:52236 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njN4x-000740-0x for larch@yhetil.org; Tue, 26 Apr 2022 11:26:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56988) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njN4k-00071l-CR for guix-patches@gnu.org; Tue, 26 Apr 2022 11:26:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46369) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njN4k-0000vK-3U for guix-patches@gnu.org; Tue, 26 Apr 2022 11:26:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njN4j-0008QC-QZ; Tue, 26 Apr 2022 11:26:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55128] [PATCH] gnu: Add r-affixcan. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 15:26:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 55128 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55128@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.165098671932318 (code B ref -1); Tue, 26 Apr 2022 15:26:01 +0000 Received: (at submit) by debbugs.gnu.org; 26 Apr 2022 15:25:19 +0000 Received: from localhost ([127.0.0.1]:40266 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njN43-0008PC-GV for submit@debbugs.gnu.org; Tue, 26 Apr 2022 11:25:19 -0400 Received: from lists.gnu.org ([209.51.188.17]:60402) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njN41-0008P4-MW for submit@debbugs.gnu.org; Tue, 26 Apr 2022 11:25:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56808) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njN41-0006QF-Ft for guix-patches@gnu.org; Tue, 26 Apr 2022 11:25:17 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:59731) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njN3y-0000g0-MQ for guix-patches@gnu.org; Tue, 26 Apr 2022 11:25:16 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 4CFFEA0184 for ; Tue, 26 Apr 2022 17:25:09 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1650986708; x=1652801109; bh=Ir4XHACFTPlZgmVmJo2ijIU23MZ7GXtgsx3VO8wgLME=; b=YDH16t/SUmhF dARGAACikxpn+vpOs0ZjV52KDEqvQ5x8mBpvAtlMdrtwiMj1NXKDG17kU3tU0hFR orA6T+tg6/I+IaJLcmoZ/hmc+cLfQrhwoFz1IJsrSClO+s+4IU5nd9HK3lit+nfn xzukzftUjPLbswspoBtAmtb0ME2fe/Y= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 1Ep8uvgTtfMX for ; Tue, 26 Apr 2022 17:25:08 +0200 (CEST) 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 for ; Tue, 26 Apr 2022 17:25:08 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2375.24; Tue, 26 Apr 2022 17:25:07 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Tue, 26 Apr 2022 17:24:55 +0200 Message-ID: <20220426152455.17387-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-14.0.0.3092-9.0.1000-26858.000 X-TM-AS-Result: No-10--6.779400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCwyLlxWhS9T9iOwf9uRq1AiycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgNedi3nDhxyOAdc X2zDkOeiAqwXSxSoYzf9znWNVSI55Z+zSGB7rwH1prOiCoANhuNYzeFjMK+No= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.779400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26858.000 X-TM-SNTS-SMTP: B14D5FA27A1E9C2E9C08F2959EE11FEEDDC4C9A2E20A6F783C79525FA0330B6D2000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1650986777; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=pznJ0OnrwcwcHmG6LPHuKAiDk2XZO+tsjEIz36Cbb7s=; b=gAfTqVccv+efz8uTrJuSpp56Kb2oP9hlH2i8Mbz9lMl0guXd8j6atdTgmvMlNse9oZ5Lpe mS5yNrPBwTy+a6lZgQbmWh5EMwoEqRG8+UOnMSI1U6rsmIal+2QAzHjDQ5IyCxgfeLVcKl 2X1RMaBqP730EAFE8ioQ9lj2zKhe1YlWK1Z5WFH6ey+Y0yQ+Z7dE10FeTjUiZpHs14XjHe 9VDWWro/PahSmKEWRonvDGjEBF/x5NABShMGRsgDrWksw37BSp7s8KB8cp0RY4BlbqmudV oj9yFePwbI9HFxlZESa2OENjLt1WfjKJwv49ccpqAB8wpYuLMb7AkoW07EMeFA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1650986777; a=rsa-sha256; cv=none; b=e7BjJqW+LMeMKPQH/UwGNljy9m5Kn3Ih+luSMlFG1x9t5+uEo+YRZ/wSwcllK1dlV03kcA EzjVqiE7uLn0LO3OcpWSsZdIIu4ooVj71SjS0xYP69aRls2YQhqMq5kv9OUtaM35k7ud+e IWZpy6vtXaikkkMCXRVK+kYyncwsqKPQclwTqX2uxoS41m7oY9OlDw1JdVDbz+l5x0cGpD 3Idh+466NkSUadXJbvlNhnawC1WSs6Q6rlqcLsdXo498TmbpZLRW0LlZKzMGQKVKnpo0+X fW1dtZPB9+2YK+v1HenlBhmvjmVT8yAa0Sfky/49WScC3QLd9CBUy+gly+D+cQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b="YDH16t/S"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.89 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b="YDH16t/S"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: A54D1264CA X-Spam-Score: 6.89 X-Migadu-Scanner: scn1.migadu.com X-TUID: sottHIQlpj0y * gnu/packages/bioconductor.scm (r-affixcan): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa862d736f..925ebcdbdc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1616,6 +1616,31 @@ (define-public r-adam functionally associated genes} (GFAG).") (license license:gpl2+))) +(define-public r-affixcan + (package + (name "r-affixcan") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AffiXcan" version)) + (sha256 + (base32 + "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d")))) + (properties `((upstream-name . "AffiXcan"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-crayon r-multiassayexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AffiXcan") + (synopsis "Functional approach to impute genetically regulated expression") + (description + "The @code{AffiXcan} package imputes a @dfn{Genetically regulated +expression} (GReX) for a set of genes in a sample of individuals, using a method +based on the @dfn{total binding affinity} (TBA). Statistical models to impute +GReX can be trained with a training dataset where the real total expression +values are known.") + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 30ff557bd7255dddec16f4a032e58f5a88d5e448 -- 2.34.0