From patchwork Tue Aug 20 08:07:04 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Navid Afkhami X-Patchwork-Id: 30216 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 86FA527BBEA; Tue, 20 Aug 2024 09:10:33 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_VALIDITY_CERTIFIED, RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 955D227BBE9 for ; Tue, 20 Aug 2024 09:10:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1sgJwb-0001I4-7X; Tue, 20 Aug 2024 04:10:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sgJwZ-0001Ho-Nw for guix-patches@gnu.org; Tue, 20 Aug 2024 04:10:20 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1sgJwZ-0001HK-E7 for guix-patches@gnu.org; Tue, 20 Aug 2024 04:10:19 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:Date:From:To:Subject; bh=s79y8cfpw9bKk+e7geRQW5Zg6tMS6CZJ4zjiIFAaP+Q=; b=NS7hDbcRSfZ4sD+9dvLHWfRVcJVG0RX6Pjy6wZaV+18BJx9h3sp7V5PdbjcfNkiDBZzguHIFoz9lF5m49g8Z/WX1FZgBT64u2pmn99OWRIY9tDzg059Fjoypu0dGlO6xUpah//+vKvVCRA7joSUw479dhr4zHU7d9zwsSFO1ULsU/Hmko9LyD5cTp/Ha9meUsqKW92XjmeKS/oHrvuO0eRDoRTMOYWnVk2XP3ws9FXy3cY8149aAEd45bsspTbtRkU8ZSRnMLaXBnuMdPrF9jNrwpwWeJ+u6+LzkR9Z1nxgFFDiZvWxOFhI0l8T+AAZ89+l+kWRj4lISVI8Kfjvu6g==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1sgJxF-0001pM-So for guix-patches@gnu.org; Tue, 20 Aug 2024 04:11:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#72727] [PATCH] gnu: Add r-spacexr. Resent-From: "Afkhami, Navid" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 20 Aug 2024 08:11:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 72727 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72727@debbugs.gnu.org Cc: "Afkhami, Navid" X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.17241414286959 (code B ref -1); Tue, 20 Aug 2024 08:11:01 +0000 Received: (at submit) by debbugs.gnu.org; 20 Aug 2024 08:10:28 +0000 Received: from localhost ([127.0.0.1]:59785 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sgJwh-0001oB-Ln for submit@debbugs.gnu.org; Tue, 20 Aug 2024 04:10:27 -0400 Received: from lists.gnu.org ([209.51.188.17]:47762) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sgJwf-0001o3-GR for submit@debbugs.gnu.org; Tue, 20 Aug 2024 04:10:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sgJvy-0001E7-DF for guix-patches@gnu.org; Tue, 20 Aug 2024 04:09:42 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sgJvw-00010N-4e for guix-patches@gnu.org; Tue, 20 Aug 2024 04:09:42 -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=1724141373; x=1725955774; bh=YUD8PJifIxjVAl/ RFH/784rt+1LZYT4s6SMDY55tWxU=; b=bBrOGNjzMjFZnnnhvZyCK/jNEC0O289 OV5MTgZmc810EXLDlLZw6MzlH/30NrMqUUohqKvPlSwEkpgyZ5OvGmyP8tDh7Mh4 uBjh/Tf+EvBcujrYgAj1Fyjhp8mSWC9FIy6Ub2dYT/hXl6pZiuNEYnccJKzCqntW qY7eU3ESsctc= Received: from SW-IT-P-EX1.mdc-berlin.net (mgw1.mdc-berlin.de [141.80.113.54]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4F8C21601E9 for ; Tue, 20 Aug 2024 10:09:30 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1544.11; Tue, 20 Aug 2024 10:09:30 +0200 From: "Afkhami, Navid" Date: Tue, 20 Aug 2024 08:07:04 +0000 Message-ID: <02122b27950c60f55dbfa860ebaf750c7ba8a360.1724141223.git.Navid.Afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28606.005 X-TM-AS-Result: No-10--5.152400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcNYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUXJ5suMuDH9GX7N8/O92sJRFj276yv/MdYBS4BO08ckNf0iqNWpSwuD4mDuxB3OdogyC DHnWW5JQMkbHh8hhHAEF0fWsfQ90fVXS3CAt+DxgarEv/I2gPylwJ057ljktmGJuJCTvCT4nRSb yPS2HFd9kALSJb7SMtz/1rSrj2fS726NrOfSk4Jd+ASoAwVB/kzCL1h4GDG+F6YYT/WTR2qQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.152400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28606.005 X-TM-SNTS-SMTP: D9E3D4477076FD3A733F1A3BE7154170B7786C42B36F75718117F2C3850714EA2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-spacexr): New variable. Change-Id: Icf2a7dd9d637d14d835c7a428093ba8daf25e25a --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) base-commit: 58faaf4eaadafa09a97ab31103eb54bd2076a699 prerequisite-patch-id: dc2f4964edf0016b1e572e9f41129606c4fb3132 prerequisite-patch-id: 4ce0ef474ba0015be3d30c7eec8f094098beaec7 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eae0a29b90..56188309a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22662,6 +22662,51 @@ (define-public r-catch value of physical insulation between neighboring domains.") (license license:gpl2+)))) +(define-public r-spacexr + (let ((commit "0a0861e3d1e16014a20e9b743d0e19d3b42231f3") + (revision "1")) + (package + (name "r-spacexr") + (version (git-version "2.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dmcable/spacexr") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hqrllzq2hi6dsr8nykn1yp7s3rcbjrv3m624b61n4nxnzza458a")))) + (properties `((upstream-name . "spacexr"))) + (build-system r-build-system) + (propagated-inputs (list r-compquadform + r-data-table + r-doparallel + r-dplyr + r-fields + r-foreach + r-ggplot2 + r-knitr + r-locfdr + r-matrix + r-metafor + r-mgcv + r-pals + r-quadprog + r-readr + r-reshape2 + r-rfast + r-rmarkdown + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/dmcable/spacexr") + (synopsis + "Cell type identification and differential expression in spatial transcriptomics") + (description + "This package is used for cell type identification in spatial transcriptomics. +It also handles cell type-specific differential expression.") + (license license:gpl3)))) + (define-public r-spectre (let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a") (revision "1"))