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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288501096 (code B ref 48575); Fri, 21 May 2021 20:28:10 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:30 +0000 Received: from localhost ([127.0.0.1]:37743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk1-0000HW-TP for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:30 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:51739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjP-00009v-Mk for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:52 -0400 Received: by mail-wm1-f53.google.com with SMTP id u133so11744900wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:51 -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=lPuLYewpgN20jwOxUL7MSEqfXRTrg+VQAJuLQemUoK0=; b=FmnTpyn2gXGIZQgih2hyJpiH/rAa5yvYIb4l+5A1HqpDVm+vgTl8stLOKAeislSSh1 fDPZu7376iO9DZzupPJ8rfMrxnIqoV15ZFylkrMmnhSRs73oZZ0jBRvxj3MjgHSylb2a tnJm/HEExcFmibjd0dhnBcgpjZxtmfLCjChwon0fbcNb8hAQF3zqRJRzwtD6xyFh+juc 8U+mpW1Vgv2s+wATIGlBMkqAKL/5yrJiCiJTNqSnhPl7uzXUHB03dM41uNGTm689izMN GO0EfWhiiE12MBApyQs16pOccNzL79OKOCWtU+DfMHDbky8bYyWLVOVw+ZdYfpta52+b 5lAg== 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=lPuLYewpgN20jwOxUL7MSEqfXRTrg+VQAJuLQemUoK0=; b=FQZccox8SztW2fsGZVkiJfRZuGqJUuSHE4GY1BNSQQuKw1BxO1zwXw98c7+CQWxDyM lYBs7FeJqpm2nBKCPc5Od83iogTFSJ2M8wYQbScOTPvRYDwextUsdICBl2Kmpmv/31up qE2V9ieOnDq7H952rPt/sRv95MnY3UolWGdsO52Tin3nwbxj/ubAJualRNB9pYm2jZuC 1ING8mCKi66FCkmV7tRREIfMc70qOV7KNyLJOivyRcXaLwch2lGy0yMspmchwE4xu0fk P6huMSzLOaZMBZiJGQJrTZUnVQrSFg+LjA+UbOaUTIerotJeDaVp+wyQuLMHkPLpAqrP APnw== X-Gm-Message-State: AOAM532Kb7U7nEuB0pDEgaptggh2/Y//p8u4XJFgglzaxSgul6B9s9tD jxKSDQs/1yqMZuuq5/SwLkJPaOS+8SI= X-Google-Smtp-Source: ABdhPJxV9/r6i/FA1Rfx4raON20gCZzXyfNt1qwJS7scyEfXkRplznmuP5f0PMLLhOOpDPUR4VCpIA== X-Received: by 2002:a7b:c3d4:: with SMTP id t20mr9932051wmj.13.1621628806170; Fri, 21 May 2021 13:26:46 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:45 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:56 +0200 Message-Id: <20210521202622.26591-24-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ee670e858..f6d3ef897a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2294,6 +2294,37 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage + (package + (name "r-gage") + (version "2.40.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5dacf8a342..daf1fb6958 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,37 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage - (package - (name "r-gage") - (version "2.40.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gage" version)) - (sha256 - (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) - (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" - "articles/10.1186/1471-2105-10-161")) - (synopsis "Generally applicable gene-set enrichment for pathway analysis") - (description - "GAGE is a published method for gene set (enrichment or GSEA) or pathway -analysis. GAGE is generally applicable independent of microarray or RNA-Seq -data attributes including sample sizes, experimental designs, assay platforms, -and other types of heterogeneity. The gage package provides functions for -basic GAGE analysis, result processing and presentation. In addition, it -provides demo microarray data and commonly used gene set data based on KEGG -pathways and GO terms. These functions and data are also useful for gene set -analysis using other methods.") - (license license:gpl2+))) - (define-public r-genomicfiles (package (name "r-genomicfiles")