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Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 23 Jun 2023 13:50:06 +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=B64250.168752818827895 (code B ref 64250); Fri, 23 Jun 2023 13:50:06 +0000 Received: (at 64250) by debbugs.gnu.org; 23 Jun 2023 13:49:48 +0000 Received: from localhost ([127.0.0.1]:37943 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAZ-0007Fp-QD for submit@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:48 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34055) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qChAH-0007Dj-Ve for 64250@debbugs.gnu.org; Fri, 23 Jun 2023 09:49:30 -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=1687528163; x=1689342564; bh=TdWMgzNHqn9HxVueSavSEd/0GtopxhbcnDMeWnYwAu8=; b=n5ElqFrH+exz EdYJQSKPo+avNfQmHlMqC9rGN5PzfCsDJ/e33I/domowGCIEKpLL5P2ORh1Im3ny V2/0ZPoAg9xI3VZGk2l/pXzEIEz6+OL8pJpRuO0KCPkVhP0mm12dKBTJAnVkJecD SGRepEkLZn/rwmPzhYcbYUlsx+Ml/X4= 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 c2062.mx.srv.dfn.de (Postfix) with ESMTPS id D55863001A3 for <64250@debbugs.gnu.org>; Fri, 23 Jun 2023 15:49:23 +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 15:49:23 +0200 From: Navid Afkhami Date: Fri, 23 Jun 2023 13:48:55 +0000 Message-ID: <136afa3705c111fa1e341c41b9ef84edf22a1fcf.1687527675.git.navid.afkhami@mdc-berlin.de> 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--3.105100-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6vybt3bgNxoI06Sf95fXiV1wa5O54mQ0iv7G DbroLG9qqpvQgIDqq9l9lT2CKLCMpKWxJDoeFc5erm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGtf/SIq+QYRp5Q4jLKq41cFYOj+cr+VeWr9rHtxF/vblftV+Cd++ggTsxjjZLfWmyI+EB 04+3Wjji5vnl1W74/FdYcen6jnu2uM2GbTpTbWTeFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJ m2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.105100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27708.007 X-TM-SNTS-SMTP: 039FFDC877E570DBC6FCC547011269FA0D1108FC841D4F9A1A6423E38FA15FC32002: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/bioconductor.scm (r-cellid): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 00701c4463..78cab7171b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1436,6 +1436,50 @@ (define-public r-celldex single-cell data or deconvolution of bulk RNA-seq.") (license license:gpl3))) +(define-public r-cellid + (package + (name "r-cellid") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CelliD" version)) + (sha256 + (base32 + "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) + (properties `((upstream-name . "CelliD"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table + r-biocparallel + r-fastmatch + r-fgsea + r-ggplot2 + r-glue + r-irlba + r-matrix + r-matrixstats + r-pbapply + r-rcpp + r-rcpparmadillo + r-reticulate + r-rtsne + r-seurat + r-stringr + r-tictoc + r-singlecellexperiment + r-summarizedexperiment + r-umap)) + (native-inputs (list r-knitr r-scater)) + (home-page "https://bioconductor.org/packages/CelliD") + (synopsis + "Single cell gene signature extraction using multiple correspondence analysis") + (description + "CelliD is a clustering-free method for extracting per-cell gene signatures from scRNA-seq. +CelliD allows unbiased cell identity recognition across different donors, +tissues-of-origin, model organisms and single-cell omics protocols. The +package can also be used to explore functional pathways enrichment in +single cell data.") + (license license:gpl3))) + (define-public r-champdata (package (name "r-champdata")