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Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 23 Jun 2023 13:50:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64250 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <64250@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 64250-submit@debbugs.gnu.org id=B64250.168752818927909 (code B ref 64250); Fri, 23 Jun 2023 13:50:07 +0000 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:49 +0000 Received: from localhost ([127.0.0.1]:37947 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAb-0007Fz-3Y for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:49 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38085) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAJ-0007Dx-Qh for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:32 -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=1687528166; x=1689342567; bh=ph27Qh8fZWanuCHXpXMtmx9rR5VMzw2t3xy6Lima8ZA=; b=DFBz3FUyaG2C Dk/v7vULmKbVsb66SzZWLuVm8hq82XNhIwD+Uq1qGlQ5McqikEBFy3mDdeJF0nQu UBQUJUGBs9t3PBS01dkRYO9p0bcGb6FO5Cg8t/YPSBOAhmx3xv/zXcUnmiWXtlBm 6ZKkBo7/46hcF1WCa+uTztkVCLaQpyo= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 0433B160239 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:26 +0200 (CEST) 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 15.1.2507.27; Fri, 23 Jun 2023 15:49:25 +0200 From: Navid Afkhami Date: Fri, 23 Jun 2023 13:48:57 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: 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-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-AS-Result: No-10--1.769400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIECxZTVRS20SJEb gebEoSmUSdh6xz9sQYzYU67xNGCLSGLfMLzDH98yBQTHl0mqX8ULixrsCJ1jTIpz++XQI8PGeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DGrZ5qG+v8TKpGmd7F6KLEiS4iQwN8o8DIutT yzubotouiqUDhDVnirc6W0J1PcPWd/+maJ+xpzkzhejr/nUAeKci6fSEqtWU2uLCTjzz6qi2qQa z8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.769400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: D8B74BA8F79B7C19F4D380FC09111963B7852D9338D72AD85718E7D60CB334E32002: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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-nichenetr): New variable. --- gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87e7c33b90..9de0470f7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14800,6 +14800,63 @@ (define-public r-liana interaction inference from scRNA-seq data.") (license license:gpl3)))) +(define-public r-nichenetr + (let ((commit "cc3bcedfd6271df2e8ca85c8b771f7faa914cd3d") + (revision "1")) + (package + (name "r-nichenetr") + (version (git-version "1.1.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saeyslab/nichenetr") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jxkrk7cpwx0lbbgjrd885jxahdgk9ysfqp2drq22g486k6p2s9y")))) + (properties `((upstream-name . "nichenetr"))) + (build-system r-build-system) + (propagated-inputs (list r-caret + r-catools + r-circlize + r-complexheatmap + r-cowplot + r-data-table + r-diagrammer + r-dicekriging + r-dplyr + r-e1071 + r-emoa + r-fdrtool + r-ggplot2 + r-ggpubr + r-hmisc + r-igraph + r-limma + r-magrittr + r-matrix + r-mlrmbo + r-parallelmap + r-purrr + r-randomforest + r-readr + r-rocr + r-seurat + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/saeyslab/nichenetr") + (synopsis "The R implementation of the NicheNet method") + (description + "The goal of NicheNet is to study intercellular communication from a computational perspective. +NicheNet uses human or mouse gene expression data of interacting cells +as input and combines this with a prior model that integrates existing +knowledge on ligand-to-target signaling paths. This allows to predict +ligand-receptor interactions that might drive gene expression changes +in cells of interest.") + (license license:gpl3)))) + (define-public r-circus (package (name "r-circus")