From patchwork Thu Jul 28 21:38:58 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 41046 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 A0CB827BBEA; Thu, 28 Jul 2022 22:42:31 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5BAC327BBE9 for ; Thu, 28 Jul 2022 22:42:31 +0100 (BST) Received: from localhost ([::1]:39028 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oHBH4-00075d-IF for patchwork@mira.cbaines.net; Thu, 28 Jul 2022 17:42:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42106) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oHBEh-0005Kh-Fq for guix-patches@gnu.org; Thu, 28 Jul 2022 17:40:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41530) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oHBEh-0007PB-3e for guix-patches@gnu.org; Thu, 28 Jul 2022 17:40:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oHBEg-0002vw-OT for guix-patches@gnu.org; Thu, 28 Jul 2022 17:40:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56819] [PATCH 1/2] gnu: Add r-phyclust. References: <3f5cff2631864372b7a0b1233e11ce86@mdc-berlin.de> In-Reply-To: <3f5cff2631864372b7a0b1233e11ce86@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Jul 2022 21:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56819 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56819@debbugs.gnu.org> Received: via spool by 56819-submit@debbugs.gnu.org id=B56819.165904438311220 (code B ref 56819); Thu, 28 Jul 2022 21:40:02 +0000 Received: (at 56819) by debbugs.gnu.org; 28 Jul 2022 21:39:43 +0000 Received: from localhost ([127.0.0.1]:59512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE8-0002uf-H0 for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:43 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34007) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE0-0002u7-UV for 56819@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:22 -0400 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; s=mdc; t=1659044353; x=1660858754; bh=UZeoarDbp/stkp/ s/bw5lJi4xmFvf5zS63vp9tkFLho=; b=F0Ge0RMbaEarUsqAgn+r1hhXJTKvMGs AwZNwNhVgEiEyWUprT++qqaBRZDDN3qv/Nr12qDYjKAHKh8BgrkeOgnkwAZYF0DW bRXVF+luhFQTo/uWBSIdGLkb2LduSt8yfqndav2bAD8hVuoEtLOoAAUlTUfC9m5l Roz9FkrBd7zY= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id E0531300317 for <56819@debbugs.gnu.org>; Thu, 28 Jul 2022 23:39:13 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 28 Jul 2022 23:39:13 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 28 Jul 2022 23:38:58 +0200 Message-ID: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-AS-Result: No-10--5.870000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57MXjfR3d0weRpYkvtv1NL4WXDP v05mLM2E+bgIM/tOpHc3AAUMpO5epWi8Qip68Ngc7lKkz03w06+uLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKcCe26BkR9xPoGRyAacnhabEnkALH5vYFtEOVr2nHEpcCjBud3XrBhH4UzdvTFUewX7cG d19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.870000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-SNTS-SMTP: 7A1D9660CBCE2E8CA1D5EA747232C574215C2E5E13122A5DB17276FF9E1DE87D2002:F 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/cran.scm (r-phyclust): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) base-commit: bdb2e262fcbea76de807cd829c2d2270661546a5 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 731facb4e5..e63cb28e19 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11699,6 +11699,31 @@ (define-public r-nleqslv singular or ill-conditioned Jacobian.") (license license:gpl2+))) +(define-public r-phyclust + (package + (name "r-phyclust") + (version "0.1-30") + (source (origin + (method url-fetch) + (uri (cran-uri "phyclust" version)) + (sha256 + (base32 + "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p")))) + (properties `((upstream-name . "phyclust"))) + (build-system r-build-system) + (propagated-inputs (list r-ape)) + (home-page "https://snoweye.github.io/phyclust/") + (synopsis "Studying phyloclustering and exploring DNA sequence data") + (description + "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous +time Markov Chain model-based approach to identify population structure from +molecular data without assuming linkage equilibrium. The package @code{phyclust} +provides a convenient implementation of phyloclustering for DNA and SNP data, +capable of clustering individuals into subpopulations and identifying molecular +sequences representative of those subpopulations. It is designed in @code{C} for +performance and interfaced with @code{R} for visualization.") + (license license:gpl2+))) + (define-public r-physicalactivity (package (name "r-physicalactivity") From patchwork Thu Jul 28 21:38:59 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 41045 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 0B06427BBEA; Thu, 28 Jul 2022 22:40:27 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 728C027BBE9 for ; Thu, 28 Jul 2022 22:40:26 +0100 (BST) Received: from localhost ([::1]:36656 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oHBF3-0005MF-KZ for patchwork@mira.cbaines.net; Thu, 28 Jul 2022 17:40:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42108) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oHBEh-0005Ki-Fo for guix-patches@gnu.org; Thu, 28 Jul 2022 17:40:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41531) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oHBEh-0007RW-5T for guix-patches@gnu.org; Thu, 28 Jul 2022 17:40:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oHBEg-0002vm-5n; Thu, 28 Jul 2022 17:40:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Thu, 28 Jul 2022 21:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56819 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56819@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 56819-submit@debbugs.gnu.org id=B56819.165904436311193 (code B ref 56819); Thu, 28 Jul 2022 21:40:02 +0000 Received: (at 56819) by debbugs.gnu.org; 28 Jul 2022 21:39:23 +0000 Received: from localhost ([127.0.0.1]:59510 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE3-0002uR-3M for submit@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47021) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oHBE0-0002u8-UU for 56819@debbugs.gnu.org; Thu, 28 Jul 2022 17:39:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1659044354; x=1660858755; bh=egkAkUi9IUru4H216Fl/W4CYeBYCPeLsNqUxt7XKvGI=; b=YVDxlLcms0jO 5FCFwUcwBtGugD6iiegDwXEpdbEzvfZ6rEYPU8W0xiCqCvAFgNwgAt2yzmifONlO AhIyBiogtnFh8LjipmeQJ06AlweLPDO31qndWzRW4NTkK9GCnaSQHMNBZHQMfbgK 1tbPuGmo1t8iuESH4IxjgATnzp9kJAQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id B8C6030031C for <56819@debbugs.gnu.org>; Thu, 28 Jul 2022 23:39:14 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 28 Jul 2022 23:39:13 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 28 Jul 2022 23:38:59 +0200 Message-ID: <20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> References: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-AS-Result: No-10--0.353900-5.000000 X-TMASE-MatchedRID: HRm6Pbbemxf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEObH aDxe+U4pMecv2pRSXP/uNT8xdcEnQwE+dA3RWUSvnMRCqQzD5eeTIp+F7SfdPaWq3wF1koS+3Zz X3J+8J0KOXcmvTm49paCaZ3gvLsy8L/fdNahJQfqRgPzABkqxIKn/3nyhTdZwm1Z19KV0SXAX3r 77y8r98b++B3z986tGSsWvYVVnFvdvCIuDq0C/xd0KiTeJteVB64sVlliWKx8fE8yM4pjsDwtuK BGekqUpOlxBO2IcOBaAGZzlhUDRC081g186HgamKXw1QgjixPsUJKrs0WIMt7IvxdQvOys8oXMO sLGOr0eqpKwlSEtl+j+p2vr9Vw2VLh4l4HGge97fImrURI36QxPJ2/Q8HUOAto20mm9aYNFI8Ra cJ+d0jn4Y+QmZJksi X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.353900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27044.002 X-TM-SNTS-SMTP: 958CF1388B2CE12B70C9D201770B1EEEC3788C592D50A34E5219A5F5320D32E42002:F 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-infercnv): New variable. --- gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31484799b2..e9bfbed9b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) + #:use-module (gnu packages python) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) @@ -2647,6 +2648,65 @@ (define-public r-ideoviz arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-infercnv + (package + (name "r-infercnv") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "infercnv" version)) + (sha256 + (base32 + "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + (properties `((upstream-name . "infercnv"))) + (build-system r-build-system) + (inputs (list python)) + (propagated-inputs + (list r-ape + r-argparse + r-biocgenerics + r-catools + r-coda + r-coin + r-digest + r-doparallel + r-dplyr + r-edger + r-fastcluster + r-fitdistrplus + r-foreach + r-futile-logger + r-future + r-ggplot2 + r-gplots + r-gridextra + r-hiddenmarkov + r-leiden + r-matrix + r-paralleldist + r-phyclust + r-rann + r-rcolorbrewer + r-reshape + r-rjags + r-singlecellexperiment + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/broadinstitute/inferCNV/wiki") + (synopsis "Infer copy number variation from single-cell RNA-Seq data") + (description + "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify +evidence for somatic large-scale chromosomal copy number alterations, such as gains +or deletions of entire chromosomes or large segments of chromosomes. This is done +by exploring expression intensity of genes across positions of a tumor genome in +comparison to a set of reference \"normal\" cells. A heatmap is generated +illustrating the relative expression intensities across each chromosome, and it +often becomes readily apparent as to which regions of the tumor genome are +over-abundant or less-abundant as compared to that of normal cells.") + (license license:bsd-3))) + (define-public r-iranges (package (name "r-iranges")