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Reply-To: bug#56147 <56147@debbugs.gnu.org> Date: Sat, 21 Jun 2025 10:14:57 +0000 retitle 56147 [PATCH] gnu: Add r-aspli. reassign 56147 guix-patches submitter 56147 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 56147 normal tag 56147 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Jun 22 10:46:36 2022 Received: (at submit) by debbugs.gnu.org; 22 Jun 2022 14:46:36 +0000 Received: from localhost ([127.0.0.1]:36276 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o41cp-0003BX-UK for submit@debbugs.gnu.org; Wed, 22 Jun 2022 10:46:36 -0400 Received: from lists.gnu.org ([209.51.188.17]:36220) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o41cl-0003BB-Kg for submit@debbugs.gnu.org; Wed, 22 Jun 2022 10:46:34 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35562) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o41cl-0003bJ-3X for guix-patches@gnu.org; Wed, 22 Jun 2022 10:46:31 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:36277) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o41ci-0000Zq-Fr for guix-patches@gnu.org; Wed, 22 Jun 2022 10:46:30 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 87EBD3001FD for ; Wed, 22 Jun 2022 16:46:24 +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=1655909183; x=1657723584; bh=KZ4F7hBDWFArzYb6hqWlKkP0ueVcB+nHVCV6ISLbiXc=; b=eWHA+lZ/oxQS A5v7xcwsJpj+7n/cPi5gi1X98MK1LcOOGTb6eOLeJFVPYiTmOkRXaOTDHlk0OxE4 64SUg63q4yiF+b9sbIe19XIYbo9S6w12eSVGgMVPgCU4ycXGnsjMU3VSm8XrPFdM jjFSR18BLZOQul30s8dltpxagxgt8IQ= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 8xcqIFheCrPb for ; Wed, 22 Jun 2022 16:46:23 +0200 (CEST) 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 for ; Wed, 22 Jun 2022 16:46:23 +0200 (CEST) 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 15.1.2507.9; Wed, 22 Jun 2022 16:46:23 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-aspli. Date: Wed, 22 Jun 2022 16:46:12 +0200 Message-ID: <20220622144612.19605-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-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-14.0.0.3092-9.0.1002-26970.005 X-TM-AS-Result: No-10--7.739600-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyx26XFXSTphShYTvQxSQq0foR 6iGzRJIA8rKRlKdbyf85/HnrJ5Wet+QBNy99xduuxaW0fY4IMuPNYQxCOihTN64sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJcFwgTvxipFa9xS3mVzWUuCgZHIBpyeFpowD+ XkID5BGvFodVF6HTGodCr3+fXOKZ0XSEGdG9HhkftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.739600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-SNTS-SMTP: FA3830F55557A27E21B5B9202FE5EDE39AF06D943566E36BEA1C3BA6F21B45472002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-aspli): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..0136d268b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,54 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-aspli + (package + (name "r-aspli") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASpli" version)) + (sha256 + (base32 + "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz")))) + (properties `((upstream-name . "ASpli"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocstyle + r-data-table + r-dt + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gviz + r-htmltools + r-igraph + r-iranges + r-limma + r-mass + r-pbmcapply + r-rsamtools + r-s4vectors + r-tidyr + r-upsetr)) + (home-page "https://bioconductor.org/packages/ASpli") + (synopsis "Analysis of alternative splicing using RNA-Seq") + (description + "@dfn{AS} (alternative splicing) is a common mechanism of post-transcriptional +gene regulation in eukaryotic organisms that expands the functional and regulatory +diversity of a single gene by generating multiple mRNA isoforms that encode +structurally and functionally distinct proteins. @code{ASpli} is an integrative +pipeline and user-friendly @code{R} package that facilitates the analysis of changes +in both annotated and novel AS events. @code{ASpli} integrates several independent +signals in order to deal with the complexity that might arise in splicing +patterns.") + ;; The authors didn't specify any GPL version in description or in the + ;; sources. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 31 16:42:33 2022 Received: (at 56147-done) by debbugs.gnu.org; 31 Oct 2022 20:42:33 +0000 Received: from localhost ([127.0.0.1]:41995 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbc9-0001bo-A9 for submit@debbugs.gnu.org; Mon, 31 Oct 2022 16:42:33 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21119) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbc7-0001bg-8m for 56147-done@debbugs.gnu.org; Mon, 31 Oct 2022 16:42:31 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1667248949; cv=none; d=zohomail.com; s=zohoarc; b=oEMqf4rJGziUzJ4qhbXkrfCVV+QbEfLYHn0LsmQTJoEYcw/Z3UNQl0/D+mP5xxm5F2B/wdz24j/RdHck/l7ZkN5iqLTxfU+y9c/VgOkH8c0ACAUpOwhvcFObM/VXfUKyQmfaSdNnI0+FraELgHzbic6ar4mtNcab/jLX4fbb7Jc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1667248949; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=g6bH0rYqgWA2z3JS1BdiHnc+7iIGXm3XO+DJAVVdohF0D+axbcQi8AE2eKsp1+chcClJG18dtlC4zijZDw6nEg2flA9RvLH8OQOL5lN2u+ggQPUnNgM+PmUj6eRXHamuK4CvHBNCFZGSDYh8VfGYmzTxu1Tiv4mCUKuLmosXpt8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1667248949; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=DPjNVRegIyiT+w8ey7j3cz6XdxD5rIs2oheqq2TQTMVQp94Hp9VHqRDM32f/P3Ok BxoCmBVqT5MsLCxqMxFn7Z4GCpQ4Plf7paHEJ1wwV0hYVkeeSFllx88PVLHv94zW8bi 9x6b2x8cFZjS7tApAGYvVNO+g5IPJKnzQ3ojVew4= Received: from localhost (155-111-142-46.pool.kielnet.net [46.142.111.155]) by mx.zohomail.com with SMTPS id 1667248947209447.85430769700736; Mon, 31 Oct 2022 13:42:27 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56147-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-aspli. 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