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X-Debbugs-Cc: rekado@elephly.net Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 17:03:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 58522 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58522@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16657669394827 (code B ref -1); Fri, 14 Oct 2022 17:03:01 +0000 Received: (at submit) by debbugs.gnu.org; 14 Oct 2022 17:02:19 +0000 Received: from localhost ([127.0.0.1]:38490 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojO4h-0001Fl-Cj for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:02:19 -0400 Received: from lists.gnu.org ([209.51.188.17]:38182) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojO4f-0001Fe-Hm for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:02:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:57308) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojO4f-0004uU-13 for guix-patches@gnu.org; Fri, 14 Oct 2022 13:02:17 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:44911) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojO4Z-0002wl-TR for guix-patches@gnu.org; Fri, 14 Oct 2022 13:02:16 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1665766914; x=1667581315; bh=YDXQaS+fEvZ/YLx IIMI2WXA7dkAl9Wb7EvTocOv9Mws=; b=RXm7AREt9g0Wgjrc1mjC2LQdl9c99a5 DUMznsrwJIai3jBlxcHgvQPDEKRjyDWcFzbAI3iUYM5xUCVOGLmeQJ8bRzmmZIlK 7yOJ2dxAGcD6DXoXQ3+Z86IXqS0NjSxVRtvZEHBbjTog5PG8Q8cHGC9F8CyvqhX5 TwAKBqF286QQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DA653A033C for ; Fri, 14 Oct 2022 19:01:54 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.12; Fri, 14 Oct 2022 19:01:54 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 14 Oct 2022 19:01:42 +0200 Message-ID: <20221014170142.3204-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-AS-Result: No-10--4.228400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyp/958oU3WcDoUdFbHYUawycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgNedi3nDhxyOAdc X2zDkOeoOKrngks05hvHPZNoumDf6dInVhYcznTYpwF3/8inEQVcmoEcWbGNMBD4ChcQLPLZ5Pt X/AxRrxQ4rywCix+XU/6Rzlk2IPEQ3R/ZHQ6/0rtOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.228400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-SNTS-SMTP: 24C97931131D532DCF837AC4D504490D40997156EEA83B36E53E5AD42F7316902002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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/bioconductor.scm (r-fishpond): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) base-commit: 10d429f2fce321d8285684503094694ec3979865 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecb60f2e24..c23520175d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14522,6 +14522,44 @@ (define-public r-rgraphviz objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fishpond + (package + (name "r-fishpond") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "fishpond" version)) + (sha256 + (base32 + "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + (properties `((upstream-name . "fishpond"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-abind + r-genomicranges + r-gtools + r-iranges + r-jsonlite + r-matrix + r-matrixstats + r-qvalue + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-svmisc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/fishpond") + (synopsis "Downstream methods and tools for expression data") + (description + "The @code{fishpond} package contains methods for differential transcript +and gene expression analysis of RNA-seq data using inferential replicates for +uncertainty of abundance quantification, as generated by Gibbs sampling or +bootstrap sampling. Also the package contains a number of utilities for working +with @code{Salmon} and @code{Alevin} quantification files.") + (license license:gpl2))) + (define-public r-fithic (package (name "r-fithic")