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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 18 Jan 2022 17:55:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53349 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53349@debbugs.gnu.org Cc: zimoun Received: via spool by 53349-submit@debbugs.gnu.org id=B53349.1642528491442 (code B ref 53349); Tue, 18 Jan 2022 17:55:05 +0000 Received: (at 53349) by debbugs.gnu.org; 18 Jan 2022 17:54:51 +0000 Received: from localhost ([127.0.0.1]:51627 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n9sh1-000073-DT for submit@debbugs.gnu.org; Tue, 18 Jan 2022 12:54:51 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:55186) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n9sgm-0008WQ-BD for 53349@debbugs.gnu.org; Tue, 18 Jan 2022 12:54:37 -0500 Received: by mail-wm1-f53.google.com with SMTP id p18so29476131wmg.4 for <53349@debbugs.gnu.org>; Tue, 18 Jan 2022 09:54:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4i7syCiE81s1lg1xy/w43c4iR25z0okMEQlkn7QPGWU=; b=Q3A4yO420NfFZECwdQq5jfX8XYSwYLFgIEksCU2T5mHby/kxRazzle9bjDFNDqSsJe 67xjRirhglTrpVmYtpjHkWfmIKzT3F+exB6RlXa2ksvndlarqJ3SAjw4LHodxttcTeac kYOsUeKp+xpt0yHkOC8xFvMj2tf+GHDh5NNEFBYqPbdCfBSb93gVBGZ38qFX/6I6fTDZ 1eX//OZogL2/kxxp+OyRCgP1VxW3BbLdQo7uaun8hfT+yF1GZliNthLAITCzKjrBLq8A xMNdmSCyMovDyUQWSD5x2EvgQBF57YFjOL/KKF7jp48TXeKHgw9MxTQupQiCjajz6/+V t6Ng== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4i7syCiE81s1lg1xy/w43c4iR25z0okMEQlkn7QPGWU=; b=wSz23QulxjxTPc4liBFckr9sh2K4DrxGb4ceKKWJuueTf4h1wOUdsTZEFMcxddKEDs og0649FBom+Raye9L7MSfNkYD63Xyf9fHHspWqDJFtgpkHCXksUb6KUknziqNkLkNUzc XrIaeRdLB3cbSdWj0PVEySXIYFeBPRkfKXw77bLIrGyO/b+nqwAPKY/qEXP7UdZWjgmR UAND7iBn08YbPb0CF+2IjsFnjxmjWtOI0yAFsTHVclid2nMXlmjarFwNIK7/MIy7324H jtWzX2aTzwAbf2DoN+G6xtLjtRyNH+NGI9+73U/zDvmFNDcxn5sbu5Oyj4IWTMlPlMZv +wFg== X-Gm-Message-State: AOAM531Zav6zIHMy2joyNSpkL6cnZYez333gBuazfyFeUN1QaC7lGrGC UJuCmHdSmD64Gie8zIMEa7D71AJpB0I= X-Google-Smtp-Source: ABdhPJw6MPxC3tyA1F6mvoCm0J16pjvbry48cEroa6VEXXe6Tr89zH096Bo/X+RkhBwdSNTVRNZyjA== X-Received: by 2002:a1c:a90c:: with SMTP id s12mr21702829wme.27.1642528470522; Tue, 18 Jan 2022 09:54:30 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id v5sm2989529wmh.19.2022.01.18.09.54.29 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 18 Jan 2022 09:54:30 -0800 (PST) From: zimoun Date: Tue, 18 Jan 2022 18:54:17 +0100 Message-Id: <20220118175418.1559782-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220118175418.1559782-1-zimon.toutoune@gmail.com> References: <20220118175418.1559782-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-icellnet): New variable. --- gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6caeec80f7..b2bd7fbbc0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li -;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Felix Gruber ;;; ;;; This file is part of GNU Guix. @@ -7771,6 +7771,50 @@ (define-public r-archr "This package is designed to streamline scATAC analyses in R.") (license license:gpl2+)))) +(define-public r-icellnet + ;; v1.0 tagged in 2020, last commit contains many fixes. + ;; DESCRIPTION says Version: 0.0.0.9000. + (let ((commit "b9c05488fb8b5ea69bd560018966eaf4e25f82a") + (revision "0")) + (package + (name "r-icellnet") + (version (git-version "1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/soumelis-lab/ICELLNET") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cld7d6xqnvd0zpcpg3sx73an6vdc9divzywgnn6zxnqcd987cnw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ (chdir "icellnet")))))) + (propagated-inputs + (list r-annotationdbi + r-data-table + r-dplyr + r-ggplot2 + r-hgu133plus2-db + r-jetset + r-psych + r-reshape2 + r-rlist)) + (home-page "https://github.com/soumelis-lab/ICELLNET") + (synopsis "Transcriptomic-based framework to dissect cell communication") + (description "This packages provides a a transcriptomic-based framework +to dissect cell communication in a global manner. It integrates an original +expert-curated database of ligand-receptor interactions taking into account +multiple subunits expression. Based on transcriptomic profiles (gene +expression), this package allows to compute communication scores between cells +and provides several visualization modes that can be helpful to dig into +cell-cell interaction mechanism and extend biological knowledge.") + (license license:gpl3)))) + (define-public r-scde (package (name "r-scde")