From patchwork Mon Sep 13 14:20:27 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 32814 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 51FC927BBE3; Mon, 13 Sep 2021 15:45:14 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2, SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 0DB8827BBE1 for ; Mon, 13 Sep 2021 15:45:14 +0100 (BST) Received: from localhost ([::1]:41482 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mPnCr-0003ZF-3j for patchwork@mira.cbaines.net; Mon, 13 Sep 2021 10:45:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49970) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mPmpS-0006ML-FR for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:35000) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mPmpS-00058E-61 for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mPmpR-0008QT-Vw for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment. References: <20210913141812.521898-1-zimon.toutoune@gmail.com> In-Reply-To: <20210913141812.521898-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 13 Sep 2021 14:21:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 50570 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 50570@debbugs.gnu.org Cc: zimoun Received: via spool by 50570-submit@debbugs.gnu.org id=B50570.163154283732326 (code B ref 50570); Mon, 13 Sep 2021 14:21:01 +0000 Received: (at 50570) by debbugs.gnu.org; 13 Sep 2021 14:20:37 +0000 Received: from localhost ([127.0.0.1]:46543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPmp3-0008PK-Gf for submit@debbugs.gnu.org; Mon, 13 Sep 2021 10:20:37 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:40656) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPmp2-0008P1-3t for 50570@debbugs.gnu.org; Mon, 13 Sep 2021 10:20:36 -0400 Received: by mail-wr1-f53.google.com with SMTP id q26so14978645wrc.7 for <50570@debbugs.gnu.org>; Mon, 13 Sep 2021 07:20:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=ly/QNZgEh14QPgEdUe6C8AVzWdV9pfMVb+PmwiHdhBk=; b=q7tKMzESQczPkVuhsi9Aj8y0ZYp/neqvQ11/2AKI/+4xyT109W7N/8ufahxVHhYLgw g6R8Dt9nIm/BJChr9vWS4MDSpYMS6sZKclIVZhwGq2abtKXBWDbB94aAewkw3watVahl nZNJiCuBiK8wJ2i8TxR1brITAqxGxdy+lhBcMMNDRMX87BFKCMjNwxMXXqgPHFiVQ6Ad cOzeZIzAjGtBJ707CeDTso8C9jV3kUfFhYKwVoHvpgMGqQH+0OJQywM5etCjqtLMXJTm aByLTSUw/jVS2rAjrWf4s+qhuOO1Q58YFEX2bSjysNbbJe1yZb1jI70WtyZ0LjCvJwgb VL0g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=ly/QNZgEh14QPgEdUe6C8AVzWdV9pfMVb+PmwiHdhBk=; b=cP4lUuw+6DxdOmEe7GQmlhBPfiElEftiTMCgmd8n7KORGT4lKyBHba8WwCqobmP7dS NIjodvw5Ihon39Q6BxUzFb4Gw69lne6B3ikvbPEAyBaKvqRQiDHj6T3HPW/7D57juLS6 g24WFYj5+gy+hzeWVm/5FQgeJ79W8THW3dK1duESsRtLTMxEL1ZK9xE5LDTRwQjS/+mz fx2FcEARdqAslPlR536mq110UGrPmzOGGVyY/4DDYAsQ1TyzE3iGbOOv+15NNrVTi58P TJJ8UO9Yq73y4qrxHRVgMcvsv/ikbZAj0rxLpvICt/WNZDYC6JIpttKe/XhzIKuW6Av/ MriA== X-Gm-Message-State: AOAM530Hb0rfgWm9dG9RWZHhTRp/a1WKMMt6WM6ckmkpMMjSRM8NmXaG 6PTK4PD52ROcQAOrxiyZmc96jYcAIJ0= X-Google-Smtp-Source: ABdhPJw46uHWPc36Agl1HGEdkX7pS+36LWDHmiYANRXqWcYWqXHU+ZGotPrtuM8iUOnokEu5SXlX/g== X-Received: by 2002:adf:d1a4:: with SMTP id w4mr12953379wrc.233.1631542830329; Mon, 13 Sep 2021 07:20:30 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id j27sm1429380wms.6.2021.09.13.07.20.29 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 13 Sep 2021 07:20:30 -0700 (PDT) From: zimoun Date: Mon, 13 Sep 2021 16:20:27 +0200 Message-Id: <20210913142028.522087-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.32.0 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/bioconductor.scm (r-simplifyenrichment): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25202410e5..e59ba07d23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4236,6 +4236,46 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-simplifyenrichment + (package + (name "r-simplifyenrichment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simplifyEnrichment" version)) + (sha256 + (base32 + "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + (properties + `((upstream-name . "simplifyEnrichment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-cluster" ,r-cluster) + ("r-complexheatmap" ,r-complexheatmap) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-go-db" ,r-go-db) + ("r-gosemsim" ,r-gosemsim) + ("r-matrix" ,r-matrix) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-proxyc" ,r-proxyc) + ("r-slam" ,r-slam) + ("r-tm" ,r-tm))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jokergoo/simplifyEnrichment") + (synopsis "Simplify Functional Enrichment Results") + (description "This package provides a new clustering algorithm, binary +cut, for clustering similarity matrices of functional terms is implemeted in +this package. It also provideds functionalities for visualizing, summarizing +and comparing the clusterings.") + (license license:expat))) + + (define-public r-trajectoryutils (package (name "r-trajectoryutils") From patchwork Mon Sep 13 14:20:28 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 32813 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id DF36027BBE3; Mon, 13 Sep 2021 15:29:09 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2, SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9BA6227BBE1 for ; Mon, 13 Sep 2021 15:29:09 +0100 (BST) Received: from localhost ([::1]:45310 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mPmxI-0003Wm-OM for patchwork@mira.cbaines.net; Mon, 13 Sep 2021 10:29:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49984) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mPmpS-0006Nv-UD for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:35001) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mPmpS-00058W-HA for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mPmpS-0008Qa-CW for guix-patches@gnu.org; Mon, 13 Sep 2021 10:21:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#50570] [PATCH 2/2] gnu: Add r-presto. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 13 Sep 2021 14:21:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 50570 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 50570@debbugs.gnu.org Cc: zimoun Received: via spool by 50570-submit@debbugs.gnu.org id=B50570.163154284132337 (code B ref 50570); Mon, 13 Sep 2021 14:21:02 +0000 Received: (at 50570) by debbugs.gnu.org; 13 Sep 2021 14:20:41 +0000 Received: from localhost ([127.0.0.1]:46545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPmp6-0008PV-PE for submit@debbugs.gnu.org; Mon, 13 Sep 2021 10:20:41 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:38774) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPmp2-0008P2-Bf for 50570@debbugs.gnu.org; Mon, 13 Sep 2021 10:20:37 -0400 Received: by mail-wr1-f45.google.com with SMTP id u16so14987532wrn.5 for <50570@debbugs.gnu.org>; Mon, 13 Sep 2021 07:20:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=BNx8u5VoWHd6V2my4Rnd5c2LXZYMXWxcv+SHTttgd+o=; b=VW2673wFC2ZQdkEHAmLX0WXsZFqb5OfYMQ9rt+RygMbZ1ZclTW7IUwtR/DJRazhLil tBV8X8vCobzLTZ6Ctzpvys/8fbyaVRr6Bh77xk1cLh1Az4drdqgIB767q+uJ7+/dKy9G 7IMluIx6BfA/QHOahe+mUOKngy4ZlJK3nc9m0Ucxcpze2rN9EcLtT67HRNxbcekcnHZf 1QyfL1Vkb6xTsOHukNVxd9iXWNo8Tem9B0v3EPeqsBShwWaeNwbtDjwGcma/aNrfxH5h ND2aT8JN10G3jsCmrWTwd7AD7RzXXHiW/1h/OSsYSz+4kahJVZgPP2aLE18O/hTSPlgU tQWQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=BNx8u5VoWHd6V2my4Rnd5c2LXZYMXWxcv+SHTttgd+o=; b=Imy/7qwYH7JUd7yK0aOeI22cBzlBISlK1jw+gW+Xo3mj1rlNypfzA4kpfOHYcyfrM/ xXbej7omisH9v+i0V/G9YKa36Ljr4FzWUEl8W21+vWSlSYFnlJSu9qZYxldqAn9Y1IvB kQBxHqBQOlYQqvlFOYKxt5s66NlDKO2V9YzV2PSIuBw/7Msu3beZQwrkLKejSPgtYt2I z3cG5wNBFjHL2wYi9tyvQ4OFO3ClYp+2L20p0sD40Tk5/bi9WE2MIgBW3phulqS0Ir2C VuZ6YJaaXQI6a0lzaNIEjjIT6OgCWDTVNTSYnZQ+cVBGTpDNBzI+qqU0dXjTSVmhngF0 Z7lg== X-Gm-Message-State: AOAM533m0YE0bQo5OoccWY1+qCHCgRIV9lLvuwTgG1OxdHMIyhgwMwDm UMzi+mNK4YKMyGqViey2pu2EyF2kkpM= X-Google-Smtp-Source: ABdhPJwfcM4ERb/I00P/lmETRXgiJHl86lCMqsrjV52emwCe8jfpxOo4VY9O4EDYHEX7U9/IwsP/og== X-Received: by 2002:a5d:4f02:: with SMTP id c2mr13249262wru.10.1631542830760; Mon, 13 Sep 2021 07:20:30 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id j27sm1429380wms.6.2021.09.13.07.20.30 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 13 Sep 2021 07:20:30 -0700 (PDT) From: zimoun Date: Mon, 13 Sep 2021 16:20:28 +0200 Message-Id: <20210913142028.522087-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.32.0 In-Reply-To: <20210913142028.522087-1-zimon.toutoune@gmail.com> References: <20210913142028.522087-1-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-presto): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c3ab0ce354..647feff9ec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li +;;; Copyright © 2021 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -7417,6 +7418,39 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-presto + (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") + (revision "0")) + (package + (name "r-presto") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/presto") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8")))) + (properties `((upstream . "presto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/immunogenomics/presto") + (synopsis "Fast Functions for Differential Expression using Wilcox and AUC") + (description "This package performs a fast Wilcoxon rank sum test and +auROC analysis.") + (license license:gpl3)))) + (define-public r-snapatac (package (name "r-snapatac")