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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Q3A4yO42; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (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-Spam-Score: -2.62 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Q3A4yO42; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (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: C968E46BF0 X-Spam-Score: -2.62 X-Migadu-Scanner: scn0.migadu.com X-TUID: cUvFiqUxcVbu * 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") -- 2.34.0