From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 11 06:21:09 2024 Received: (at submit) by debbugs.gnu.org; 11 Jan 2024 11:21:09 +0000 Received: from localhost ([127.0.0.1]:58828 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNt7U-0005VL-Vp for submit@debbugs.gnu.org; Thu, 11 Jan 2024 06:21:09 -0500 Received: from lists.gnu.org ([2001:470:142::17]:43238) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNt7S-0005Ui-AL for submit@debbugs.gnu.org; Thu, 11 Jan 2024 06:21:07 -0500 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 1rNt7P-0004iT-2y for guix-patches@gnu.org; Thu, 11 Jan 2024 06:21:03 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rNt7M-0002uK-E0 for guix-patches@gnu.org; Thu, 11 Jan 2024 06:21:02 -0500 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=1704972047; x=1706786448; bh=s+E6OFaBLkQNiCn MBCpcjJ3pRcz1bpdXhrikFT2aOjk=; b=mto+yBnjdiBoMK6h5vOf1jEzUblJvqn AztTLCmiL+zzhewApoQgkiSPD3i/TxNV99bDHcpjp3qSUCPrMbW5/FphYKI6WwEk xbVIN+w3PQNLt74NtK/7k99fs0/+9CgiBkKiEcVBExqO3/OoBuCM/HR/YCfKrwxs bh0ZJh+TyQSk= 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 81FE9300124 for ; Thu, 11 Jan 2024 12:20:47 +0100 (CET) Received: from localhost (141.80.218.27) 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 15.2.1258.28; Thu, 11 Jan 2024 12:20:46 +0100 From: nafkhamdc To: Subject: [PATCH] gnu: Add r-azimuth. Date: Thu, 11 Jan 2024 11:20:43 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] 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-14.0.0.3152-9.1.1006-28112.006 X-TM-AS-Result: No-10--9.047400-5.000000 X-TMASE-MatchedRID: kREspPIIG7R6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/8Y/xikJArkjkpOkDFSV28wIdG4n3A2CkfOaYwP8dcX5IvK4LrXs1aSdEcnIP1FQIhEz I3+mkzifjF9AwiL1SNPoaAqBNgLdj7IWnvto+9Z17Ep+79T+3emMS2PfTVhK+uAzeO3IdJJBu/b jma7YlCQ3eIpJ+DD14guo0qpPe2Od3++IujRVqB+OnF2j8nBWbrixttRG+E/NTvZg4AwMmOJ4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyF82MXkEdQ77nAXQ/eXvjkNQHtyU67FjJbWyfmejphjz9RzU 4552Gdxl/nptUJXE6g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--9.047400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28112.006 X-TM-SNTS-SMTP: 4C0B64A148D826F6EDA65672F68DA8108C95BFDCF72D781B1CEF2DBB6AE3E7BF2000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: nafkhamdc X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (r-azimuth): New variable. Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03 --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f574fea0e9..9b45c54ef9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11171,6 +11171,66 @@ (define-public r-archr "This package is designed to streamline scATAC analyses in R.") (license license:gpl2+)))) +(define-public r-azimuth + (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e") + (revision "1")) + (package + (name "r-azimuth") + (version (git-version "0.5.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/azimuth") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm")))) + (properties `((upstream-name . "Azimuth"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38 + r-dt + r-ensdb-hsapiens-v86 + r-future + r-ggplot2 + r-glmgampoi + r-googlesheets4 + r-hdf5r + r-htmltools + r-httr + r-jaspar2020 + r-jsonlite + r-matrix + r-patchwork + r-plotly + r-presto + r-rcpp + r-rlang + r-scales + r-seurat + r-seuratdata + r-seuratdisk + r-seuratobject + r-shiny + r-shinybs + r-shinydashboard + r-shinyjs + r-signac + r-stringr + r-tfbstools + r-withr)) + (home-page "https://github.com/satijalab/azimuth") + (synopsis + "Shiny app showcasing a single-cell data query-reference mapping algorithm") + (description "Azimuth utilizes an annotated reference dataset. +It automates the processing, analysis, and interpretation. +This applies specifically to new single-cell RNA-seq or +ATAC-seq experiments. Azimuth leverages a reference-based +mapping pipeline that inputs acounts matrix and performs +normalization, visualization, cell annotation, and +differential expression.") + (license license:gpl3)))) + (define-public r-icellnet ;; v1.0 tagged in 2020, last commit contains many fixes. ;; DESCRIPTION says Version: 0.0.0.9000. base-commit: 6341dddcb9e7c8d555ea7294d61dcf64d775e032 -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 12 07:41:05 2024 Received: (at 68381-done) by debbugs.gnu.org; 12 Jan 2024 12:41:05 +0000 Received: from localhost ([127.0.0.1]:35111 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rOGqO-00019S-NG for submit@debbugs.gnu.org; Fri, 12 Jan 2024 07:41:05 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21054) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rOGqI-00018p-Qu for 68381-done@debbugs.gnu.org; Fri, 12 Jan 2024 07:41:02 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1705063258; cv=none; d=zohomail.com; s=zohoarc; b=epLe7lpnEjD9ckVKqNID493RiT5ss2UGvDSbI9E6+IaNg4ST5AIcR2/Xp82lOQtqFm+2MuJdA9aB4Ed9ytP60jQQvkMrbKmYlV1zT+h+07nmNvky/fAowCXS5OVZboiy2aBLZvPEr5KlqTH95TkUMBHjdLT455gctpr5qkeh+y4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1705063258; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=OEXbE2Kp9juVPueJDRsF8xTGreQ78GGMj2ZDsP+Xc/kaSG/W5Y+EgrRXWymM+Dh8JOGepEdD9/adbrXQ5QR8EChGJf1DBkj5sPNUuN1jQ3Eng6kbj2SF4iQhml/JfAan7d4oTh22xs4pkJbXpBoumgp+2FJp9GkCYYFCY0DrfLw= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1705063258; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=KxMptw9OSa8QC/3PjxJma7RFLb654W7EEt1T08PqlLTqpFfZu5z3kBakCWCtkpGo OTqL53T9yJjra8C+DJWRuwjaWVMyRskTkvOxz+nG8MBK49OJF2Jkr43gXmBl/5+YYQq HxY+nZxDBpy36jDIh0yYvUzYg0NIDsmaDv556o5o= Received: from localhost (103-108-142-46.pool.kielnet.net [46.142.108.103]) by mx.zohomail.com with SMTPS id 1705063257130123.04648409796619; Fri, 12 Jan 2024 04:40:57 -0800 (PST) User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 68381-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-azimuth. Date: Fri, 12 Jan 2024 13:40:38 +0100 Message-ID: <87o7dq4td5.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 68381-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Applied, thank you! -- Ricardo From unknown Sat Jun 21 05:20:34 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 10 Feb 2024 12:24:17 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator