From patchwork Thu Mar 2 16:48:03 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47538 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 4224016C35; Thu, 2 Mar 2023 16:49:56 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C053C16CDE for ; Thu, 2 Mar 2023 16:49:54 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pXm7j-0005QE-FD; Thu, 02 Mar 2023 11:49:43 -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 1pXm7W-0005Dz-AT for guix-patches@gnu.org; Thu, 02 Mar 2023 11:49:33 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pXm74-0007lC-4c for guix-patches@gnu.org; Thu, 02 Mar 2023 11:49:23 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pXm74-0006gq-0a for guix-patches@gnu.org; Thu, 02 Mar 2023 11:49:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61921] [PATCH] gnu: Add r-oscope. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 02 Mar 2023 16:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61921 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61921@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167777573125696 (code B ref -1); Thu, 02 Mar 2023 16:49:01 +0000 Received: (at submit) by debbugs.gnu.org; 2 Mar 2023 16:48:51 +0000 Received: from localhost ([127.0.0.1]:58260 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6s-0006gO-L9 for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:40340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6p-0006gE-SG for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:48 -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 1pXm6p-0004Ms-7y for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:47 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pXm6m-0007i4-OH for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:46 -0500 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=1677775711; x=1679590112; bh=oii7NA4gPGIAQcf Ip4urfDRritU6hfyWTIAMRrsMw9Q=; b=at5OFq2Y44aDsh5ERlakzrNDHaATXxc n6bCI/QkLOTeHOdDjh+fmkGjNJjapEdYuFdXpngDbO5vhFiFs4nRJduz5szBRDwD cHvehTRfDpjrO87oVbTE3/zjqpPTBtjwFvpZMEe2JiwayDS+fNMgC2xIv6apUuOq peY4c+ONSEUU= 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 1DE6BA0268 for ; Thu, 2 Mar 2023 17:48:30 +0100 (CET) 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 15.1.2507.21; Thu, 2 Mar 2023 17:48:30 +0100 From: Navid Afkhami Date: Thu, 2 Mar 2023 16:48:03 +0000 Message-ID: <20230302164803.71966-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.001 X-TM-AS-Result: No-10--7.627800-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIyd mby1eQX7K1OIo1kOJjPuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/F0kjYVlocoaY5ZGw7wyeHm1L VbqyavHICBvE1eIcYKmIE2wu8D/s4xGoL6ZNDLbNT3j6uyvUYPA47FdvA20VAD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58I/9UW5M5dRMpg5yOcdoVgvcUt5lc1lLgoGRyAacnhab3j9qEHCD2WKGUz 541wQvAVEps1bJtZAbBdtWJkhAMBH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.627800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.001 X-TM-SNTS-SMTP: 7E733F6A764EAE22DC12745819A03181531DBDA77CF03C29DD2AD6A3BE59ACA22002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-oscope): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bfca85bbc..c4fb44f7b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1702,6 +1702,37 @@ (define-public r-curatedtcgadata across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-oscope + (let ((commit "32e0ea72236128731f35a60fb5abcde5b5d35433") + (revision "1")) + (package + (name "r-oscope") + (version (git-version "1.29.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.bioconductor.org/packages/Oscope") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02929i7zd4fwdhxi0h2i7y3sn6v1k3srahn5a6v9wvihp5nmgcig")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://git.bioconductor.org/packages/Oscope") + (synopsis + "Oscillatory genes identifier in unsynchronized single cell RNA-seq") + (description + "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. +This statistical pipeline has been developed to identify and recover the +base cycle profiles of oscillating genes in an unsynchronized single cell +RNA-seq experiment. The Oscope pipeline includes three modules: a sine model +module to search for candidate oscillator pairs; a K-medoids clustering module +to cluster candidate oscillators into groups; and an extended nearest insertion +module to recover the base cycle order for each oscillator group.") + (license license:asl2.0)))) + (define-public r-parathyroidse (package (name "r-parathyroidse")