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Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 20 Jan 2023 08:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60955 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60955@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16742033306374 (code B ref -1); Fri, 20 Jan 2023 08:29:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jan 2023 08:28:50 +0000 Received: from localhost ([127.0.0.1]:45405 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pImlV-0001ej-WC for submit@debbugs.gnu.org; Fri, 20 Jan 2023 03:28:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:36476) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pImlT-0001ea-Fh for submit@debbugs.gnu.org; Fri, 20 Jan 2023 03:28:48 -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 1pImlR-0006jO-LQ for guix-patches@gnu.org; Fri, 20 Jan 2023 03:28:46 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pImlO-0005a8-PO for guix-patches@gnu.org; Fri, 20 Jan 2023 03:28:45 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1674203298; x=1676017699; bh=pGO8LpbPJabTGxu m9FwtxgbhKB3uuUO7G22Hoj2Qtug=; b=mEa9UfS8WFx606GmeulNf7tOxC3y31q LrUjYYUx6AjwNV6qiTtNmuuaDlT5JThk4cfTW7LPDRqWMNfD17CJZjdzz9lnauDK i9zHQYSEAuUmwc7WbSdnwYWOqTQk25M0BSA6Y+B48CAMnQBNsG8YXWioeo1SJgHq vUUcUwdF2KEY= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id E1027A02D5 for ; Fri, 20 Jan 2023 09:28:18 +0100 (CET) Received: from localhost.localdomain (10.84.128.68) 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 15.1.2507.17; Fri, 20 Jan 2023 09:28:18 +0100 From: Navid Afkhami Date: Fri, 20 Jan 2023 09:28:06 +0100 Message-ID: <20230120082806.46337-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [10.84.128.68] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27396.006 X-TM-AS-Result: No-10--6.458400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCQgqYHjJNWHeCZa9cSpBObnAuQ0xDMaXkH4q tYI9sRE/GXVOModIZ6Zte88+fSr9hsThxwOZdw6dfOaYwP8dcX5IvK4LrXs1aQjxoTu0kNRwte+ ocL7MBZfOrf5TzZFi8e90pTLJltDYq2NInS93zS99mF5tonduL7DeJMB5o2kwIpz++XQI8PGeAi CmPx4NwHJnzNw42kCxxEHRux+uk8hfNjF5BHUO+2FO3ZYnxJOs/c5iA9sXGXLXPaOEPhFXva9MF gCo2I1lDZ4IoXUId28= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.458400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27396.006 X-TM-SNTS-SMTP: AE0818BA42E4DA2321D97BC9B56686AA7E487991E748972C05508233EA305D4C2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -33 X-Spam_score: -3.4 X-Spam_bar: --- X-Spam_report: (-3.4 / 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, FUZZY_WALLET=1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 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/bioconductor.scm (r-scds): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 2 +- 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53c7d048c9..0699813af3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet +;;; Copyright © 2023 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; @@ -7266,6 +7267,33 @@ (define-public r-scannotatr cell types based on specific research needs.") (license license:expat))) +(define-public r-scds + (package + (name "r-scds") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scds" version)) + (sha256 + (base32 + "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + (properties `((upstream-name . "scds"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-matrix + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scds") + (synopsis "In-silico doublet annotation for single cell RNA sequencing data") + (description + "This is an R package for doublet annotation of single cell RNA sequencing data. +@code{scds} provides methods to annotate doublets in scRNA-seq data computationally.") + (license license:expat))) + (define-public r-scdblfinder (package (name "r-scdblfinder") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 152771a645..533f8a5f27 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,7 +23,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Felix Gruber -;;; Copyright © 2022 Navid Afkhami +;;; Copyright © 2022,2023 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;;