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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Sep 2020 16:09:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 43400 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 43400@debbugs.gnu.org Cc: zimoun Received: via spool by 43400-submit@debbugs.gnu.org id=B43400.160009969032488 (code B ref 43400); Mon, 14 Sep 2020 16:09:03 +0000 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:10 +0000 Received: from localhost ([127.0.0.1]:55980 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1W-0008Rq-Cm for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:10 -0400 Received: from mail-wm1-f41.google.com ([209.85.128.41]:32811) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1O-0008Pq-Pj for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:03 -0400 Received: by mail-wm1-f41.google.com with SMTP id e11so9189390wme.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=3AE8XJVj92n6rfCjbWovIOQdzoIyucUx0ssj7sr2pRU=; b=dwNJkg8zQeyqX92Pvure4XP8rAZApneaC7jUR5T5Z6BGVXhSClV9hPWDujoOiicQyc FJ8n7MUmxxh9eTjEMjz5o2qQfd+NlL8II23BL+3Ioc7fGnyw8/xar6h6UCPKz+iqb6DO sRYX02q5Ui3qZt4N4M6U35jrTYqa18F9upKO/5hxVMKNxNnLXVbW0MapRv9QAvKbns3I /4yQVDp3f6j2RVkQHjJ81hDOPf5ROkSP+hxHe+yFyf4i4wuTvOY7oB+h6ryBh0beYpxe DgQOCb9ZGOR0/pyRMThhIC4Jd3lwG9lLI9RFo94fA2/wPBrGNP8z1AfWu7Gy3pka4BxS 9gZQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=3AE8XJVj92n6rfCjbWovIOQdzoIyucUx0ssj7sr2pRU=; b=gndkK6Fd02Mt06dNmZa2N+GOqHwE1/DZAKX+Fd8eWWh8OloBVrrwHhtUnytdIp8ig+ KkkKPRHpJiIws4xzxClPiLwmecuS8SlCyl5x6UC67IqPDCDlLV/zckAQyrnFfNq/mMkT 97pPKo9/4QFBD4AdEuyeKG/5vpMy+72n+4buUbJitYarmAm8czerfB7W1g8SATcobhs3 1p5givOhVCjbJDpRbu2ZsOrL67LS8PgDeDYXCTKWkXU8HY85N0hroiHOsypyaoQI1Tqr cYuG00ISlAt7cZ5K/t86xI8wJitDOBxQAc5jQDuUosFYtgy2oE6BN85vxtEHQzA3EzSo ol/Q== X-Gm-Message-State: AOAM533GfirQB+iCoKYAG44Uk81GjVcS0+UY+Kxsma2hRGRvGiEAuzVj eK1Vk7Va81arJNDjIJsTwUIuGeZxjF4= X-Google-Smtp-Source: ABdhPJw+IJNgHuFHWJPjYYp5WPZgF5FUuexmjHeCtHLytwHlrKvOmGZGYmGYreCl1HTqOq18r7i7jQ== X-Received: by 2002:a1c:c2c6:: with SMTP id s189mr122234wmf.146.1600099676952; Mon, 14 Sep 2020 09:07:56 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:56 -0700 (PDT) From: zimoun Date: Mon, 14 Sep 2020 18:07:40 +0200 Message-Id: <20200914160747.8983-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) 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-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=dwNJkg8z; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 4.09 X-TUID: +R/AzMVZVOEa * gnu/packages/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e81e9cd726..77de0e2275 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8336,6 +8336,49 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-scran + (package + (name "r-scran") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scran" version)) + (sha256 + (base32 + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-bh" ,r-bh) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dqrng" ,r-dqrng) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-statmod" ,r-statmod) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/scran") + (synopsis "Methods for single-cell RNA-Seq data analysis") + (description "This package implements a variety of low-level analyses of +single-cell RNA-seq data. Methods are provided for normalization of +cell-specific biases, assignment of cell cycle phase, and detection of highly +variable and significantly correlated genes.") + (license license:gpl3))) + (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccdc693e08..dcafbb2d21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10857,49 +10857,6 @@ various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.") (license license:gpl2+))) -(define-public r-scran - (package - (name "r-scran") - (version "1.16.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "scran" version)) - (sha256 - (base32 - "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/scran") - (synopsis "Methods for single-cell RNA-Seq data analysis") - (description "This package implements a variety of low-level analyses of -single-cell RNA-seq data. Methods are provided for normalization of -cell-specific biases, assignment of cell cycle phase, and detection of highly -variable and significantly correlated genes.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0