From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms9.migadu.com with LMTPS id oPy9DkOvlWSK4AAASxT56A (envelope-from ) for ; Fri, 23 Jun 2023 16:42:11 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id MGt+DkOvlWQqZAEAauVa8A (envelope-from ) for ; Fri, 23 Jun 2023 16:42:11 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id D99FAA2ED for ; Fri, 23 Jun 2023 16:42:10 +0200 (CEST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qChAu-0001ss-LK; Fri, 23 Jun 2023 09:50:08 -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 1qChAt-0001sC-KY for guix-patches@gnu.org; Fri, 23 Jun 2023 09:50:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qChAt-0007L1-AB for guix-patches@gnu.org; Fri, 23 Jun 2023 09:50:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qChAt-0007IQ-6I for guix-patches@gnu.org; Fri, 23 Jun 2023 09:50:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64250] [PATCH 13/15] gnu: Add r-nichenetr. 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 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1687531331; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=4Tcy9CCiQsJu5zqDxezjRiuspflrp8ozPHjQ84217n8=; b=pEjS1xR9Ho6fTr9rkBnYGK7OU+s+y4val+UOB7g1BuvYX2TgWu3lPTF4mPr2zVhVVvYLDH hSm75b535FLOJw42HCO4+olxSyyqfIBNX/bM9JDLtMo6hpMIf/ZmkSnxT+BXFilbgt7Tkz 8VCSHRyUzTK7AaJT37V6KlaUgxnrzn2T+Rb7C9NJLcGrFUGudHJywJYDFpOzni9hVUTaTl ahOT4+0QXIQu3ZeSSiuTHDFLYeSZXV4L3qm1ppvewuGAhweSr+UUffaj87LAAxAqn5DPey rC36Q5mQ12QwzkyHc8arkPxeeJsi8Lhq8FNh+Y0kJpJX3CoKsw2uN5YyC/F+Lg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=DFBz3FUy; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" ARC-Seal: i=1; s=key1; d=yhetil.org; t=1687531331; a=rsa-sha256; cv=none; b=KDGMn41kgc9WQcwIcDw2lRn4/hX2iM7OenrSut1xcS2Wnu8QvYeDfDzAd064Z/uOLlhEJs ahBOWYo5jMXCd5z83JEERBIe93zi/2xy+pXGBGCxyx8Wemv3EhvEU6tO/+lyzJs7ncKgCF GC3wFKAN3Z6g9FJtv1SezTDrUfj6JqLgl3+sqHhmSDHy+RIGx7Zn5dV5Mhr09vHnICbeLW PUu8oZac4x3RrBT6R7hPlwySGiJpB0qLJ3udA3VhusvjfJb/5920eEY1sXIt1AKSg9gl34 bproKNoOeXEiLtBOYQaxdfaEvS6GoCDgJ7HvEdSztHb5z9/7SvCvttNkN1HVWQ== X-Migadu-Scanner: scn1.migadu.com X-Migadu-Spam-Score: 0.45 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=DFBz3FUy; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: D99FAA2ED X-Spam-Score: 0.45 X-TUID: ql9mnRi4wk4S * 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") -- 2.34.1