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Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 20 Jan 2023 09:56:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60959 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60959@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16742085491367 (code B ref -1); Fri, 20 Jan 2023 09:56:01 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jan 2023 09:55:49 +0000 Received: from localhost ([127.0.0.1]:45623 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pIo7h-0000Ly-Bb for submit@debbugs.gnu.org; Fri, 20 Jan 2023 04:55:49 -0500 Received: from lists.gnu.org ([209.51.188.17]:43414) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pIo7e-0000Lp-6I for submit@debbugs.gnu.org; Fri, 20 Jan 2023 04:55:47 -0500 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 1pIo7d-0001f3-P1 for guix-patches@gnu.org; Fri, 20 Jan 2023 04:55:45 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pIo7b-0004Yq-2V for guix-patches@gnu.org; Fri, 20 Jan 2023 04:55:45 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1674208537; x=1676022938; bh=WytP0TY2AWuCq30 NWabaP+e4UywjLtuvTPie8WFOYVI=; b=LrxoTRnjidpA88jDb1zBY+yqxcAvihI qNVVxPNzY3EIhytg5Vcu83wrX+hr8B1/uLrE52ZCTG9yZN1BAhsNesd6b30pmVMg rXi1K51iKPa/SLr7hpwJTjHkxiUUPmQwoZm/So6j2engepfeBZ5Ez5nFrclVSOGw A1h8zgXrlRCQ= 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 D824D300380 for ; Fri, 20 Jan 2023 10:55:37 +0100 (CET) Received: from localhost.localdomain (10.84.128.68) 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 15.1.2507.17; Fri, 20 Jan 2023 10:55:31 +0100 From: Navid Afkhami Date: Fri, 20 Jan 2023 10:55:21 +0100 Message-ID: <20230120095521.50160-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [10.84.128.68] 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-14.0.0.3092-9.0.1002-27396.006 X-TM-AS-Result: No-10--2.700200-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIEJ1hMCC63pYkYd nzk6dz7bHyjn2xyeLrGIE2wu8D/s4nH1+lINchTBvTnqYKYXTRhDkv2q7d+VDlwV2iaAfSWeDGx /OQ1GV8l1PyA7eE+Ph+gtHj7OwNO22utO5qEfOUbfoa4aLPcKNgdn1Aa5xF4jdoZIDdw8dUX0rb g6W6q4zoeoTQHYjCrHkOa06cc0gZclQlBhNjx/SfY5SJlYHI1SWgAXi7nExyXQJ88ZHP8DjvmJf 6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.700200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27396.006 X-TM-SNTS-SMTP: 3398E495132F324398CA8DE960BC9B39042FE08226B541DE69548D36F8931CC02002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-tsis): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 86d65d2031..cb5f71c40e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8215,6 +8215,37 @@ (define-public r-snapatac single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-tsis + (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc") + (revision "1")) + (package + (name "r-tsis") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wyguo/TSIS") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17c8i25iwhldvs3c51m0wny40iffm8szzijalpwrxhzbv0xa94rb")))) + (properties `((upstream-name . "TSIS"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wyguo/TSIS") + (synopsis "Time-series isoform switch of alternative splicing") + (description + "TSIS is used for detecting transcript isoform switches in time-series data. +Transcript isoform switches occur when a pair of alternatively spliced isoforms +reverse the order of their relative expression levels. TSIS characterizes the +transcript switch by defining the isoform switch time-points for any pair of +transcript isoforms within a gene. In addition, this tool describes the switch +using five different features or metrics. Also it filters the results with user’s +specifications and visualizes the results using different plots for the user to +examine further details of the switches.") + (license license:gpl3)))) + (define-public r-umi4cpackage (let ((commit "88b07d896a137418ba6c31c2474b9dbe1d86fc20") (revision "1"))