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X-Debbugs-Cc: rekado@elephly.net Date: Fri, 14 Oct 2022 19:01:42 +0200 Message-ID: <20221014170142.3204-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-AS-Result: No-10--4.228400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyp/958oU3WcDoUdFbHYUawycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgNedi3nDhxyOAdc X2zDkOeoOKrngks05hvHPZNoumDf6dInVhYcznTYpwF3/8inEQVcmoEcWbGNMBD4ChcQLPLZ5Pt X/AxRrxQ4rywCix+XU/6Rzlk2IPEQ3R/ZHQ6/0rtOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.228400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-SNTS-SMTP: 24C97931131D532DCF837AC4D504490D40997156EEA83B36E53E5AD42F7316902002: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 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-fishpond): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecb60f2e24..c23520175d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14522,6 +14522,44 @@ (define-public r-rgraphviz objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fishpond + (package + (name "r-fishpond") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "fishpond" version)) + (sha256 + (base32 + "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + (properties `((upstream-name . "fishpond"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-abind + r-genomicranges + r-gtools + r-iranges + r-jsonlite + r-matrix + r-matrixstats + r-qvalue + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-svmisc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/fishpond") + (synopsis "Downstream methods and tools for expression data") + (description + "The @code{fishpond} package contains methods for differential transcript +and gene expression analysis of RNA-seq data using inferential replicates for +uncertainty of abundance quantification, as generated by Gibbs sampling or +bootstrap sampling. Also the package contains a number of utilities for working +with @code{Salmon} and @code{Alevin} quantification files.") + (license license:gpl2))) + (define-public r-fithic (package (name "r-fithic") base-commit: 10d429f2fce321d8285684503094694ec3979865 -- 2.37.3 From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 27 09:25:37 2022 Received: (at 58522-done) by debbugs.gnu.org; 27 Oct 2022 13:25:37 +0000 Received: from localhost ([127.0.0.1]:56467 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2t7-0002b9-8H for submit@debbugs.gnu.org; Thu, 27 Oct 2022 09:25:37 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21166) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2t4-0002b0-Sh for 58522-done@debbugs.gnu.org; Thu, 27 Oct 2022 09:25:35 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1666877132; cv=none; d=zohomail.com; s=zohoarc; b=ESXIvoEGEN17MoARUaumrHnpYKlwoDjmpk9nB7BDif2kdPnnKjaYrjVtHoyF3OrflUKfcGxbFHv6vpnQ7hxhNtc5XzfXAcvPIVPhzyYTMb3ZqJEVdN67omCdEG850lA8jGtJybesKh/4d60kFZihFq//Ek0HQrEKUyzaqWzK/5I= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1666877132; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=6Yh6ekMQaQ9pqX8POHQj3ap8HuQv6vv9MXeZExD+548=; b=ezS8XVYrZTzqd0pfw92IEQeMkqTednNX4RAhKmJo9xWUItY+giVUERlmnGPpe9ty8SuhUdDGZ6YhQ6LJ6m6/qn5EwPJ3RUIWii9l/i2B0uxZZD6ZWm8z6RoPvfDk4D5zdWrRX8HSzg59Bs5jOg8zIjzA+Yl7WruyKFI9rosID04= 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=1666877132; 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=6Yh6ekMQaQ9pqX8POHQj3ap8HuQv6vv9MXeZExD+548=; b=L80DXYsb4siWyM7YvroYpCjQpAHrVgSxcRW9aWQnfYVVozS9traSaFY+MjX/gXRD Z3QzPMf4tfm2sjkVFe+hI804d/Ln1f/9mTbtcHcNUXlWeKWZRHODzRxJUDz7HBlgcZj vl6AUZwM3YwSAt6q0xYistDGWJohKCAFLPi4v8Ts= Received: from localhost (151-110-142-46.pool.kielnet.net [46.142.110.151]) by mx.zohomail.com with SMTPS id 1666877130843197.8020614204362; Thu, 27 Oct 2022 06:25:30 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 58522-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-fishpond. 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