From patchwork Fri Jan 20 08:57:59 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46298 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 7ABF627BBED; Fri, 20 Jan 2023 08:59:34 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 25AC327BBE9 for ; Fri, 20 Jan 2023 08:59:32 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pInEo-0006Lm-TA; Fri, 20 Jan 2023 03:59:06 -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 1pInEl-0006L3-HF for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:03 -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 1pInEl-0003Sz-87 for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pInEk-0004qc-Mu for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60957] [PATCH 1/2] gnu: Add r-doubletcollection. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 20 Jan 2023 08:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60957 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60957@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167420510318551 (code B ref -1); Fri, 20 Jan 2023 08:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jan 2023 08:58:23 +0000 Received: from localhost ([127.0.0.1]:45528 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pInE6-0004p7-LV for submit@debbugs.gnu.org; Fri, 20 Jan 2023 03:58:22 -0500 Received: from lists.gnu.org ([209.51.188.17]:45224) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pInE4-0004ou-06 for submit@debbugs.gnu.org; Fri, 20 Jan 2023 03:58:20 -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 1pInE3-0006FL-Oi for guix-patches@gnu.org; Fri, 20 Jan 2023 03:58:19 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pInE0-0003KD-Rp for guix-patches@gnu.org; Fri, 20 Jan 2023 03:58:19 -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=1674205092; x=1676019493; bh=fmArgrcKgkqf14Y Od+TJjheHsPTOdMqHw1qHAt4q5ag=; b=BvPpUczHnjaZ5P3pz7HpAPn40Ls/xYc /aSGwODPsiPffOtYH4pY8DWHCOxotxAdNgZMX7f6b0u5Jm/e6iI3HL+xDKJvNOOH i2L0KjOOxsx33GpdGig22GsfzxZnhwlzQUHYs5iai6ef+eBuGlA80Snx5YssP9KW wo/gLDdQYZ2g= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 125C31602D9 for ; Fri, 20 Jan 2023 09:58:11 +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 09:58:11 +0100 From: Navid Afkhami Date: Fri, 20 Jan 2023 09:57:59 +0100 Message-ID: <20230120085800.47650-1-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--5.188800-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2t6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896shuUivRMGUl1p+fe/QaxeXko12 TsqCdp+vWhKYfDziAdPPqvTEg/u81EQt7acrBPADjB2htmJXMOAqeuvkLAsKKAhn751acftuYDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07YFInLyeDAoZf+4VUP7zprw+n6EgPi9TmJdRQ +kdd8btEQD3jfHippwY8p2lAy8TBg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.188800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27396.006 X-TM-SNTS-SMTP: 2A8E1400BDC28A1A55D5E4D96751605FAA34980423734219013D1BBA3323D4862002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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-doubletcollection): New variable. --- gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36c9db90bd..86d65d2031 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7986,6 +7986,46 @@ (define-public r-chromunity Pore-C concatemers.") (license license:gpl3)))) +(define-public r-doubletcollection + (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd") + (revision "1")) + (package + (name "r-doubletcollection") + (version (git-version "1.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/xnnba1984/DoubletCollection") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02cvibyc2nwc4037ramm5cskjwyrb9ib9hkrfhmvhbslkn5ixz1v")))) + (properties `((upstream-name . "DoubletCollection"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-doubletfinder + r-gam + r-ggplot2 + r-ggthemes + r-mast + r-mclust + r-prroc + r-reticulate + r-scales + r-scdblfinder + r-scds + r-seurat + r-singlecellexperiment + r-slingshot + r-summarizedexperiment)) + (home-page "https://github.com/xnnba1984/DoubletCollection") + (synopsis "Tool for finding doublets in scRNA-seq data") + (description + "This is an R package that integrates the installation of doublet-detection methods. +In addition, this tool is used for execution and benchmark of those eight mentioned methods.") + (license license:gpl3+)))) + (define-public r-pando (package (name "r-pando") From patchwork Fri Jan 20 08:58:00 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46299 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 03AC727BBED; Fri, 20 Jan 2023 08:59:48 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,FUZZY_WALLET,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 EA34A27BBE9 for ; Fri, 20 Jan 2023 08:59:46 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pInEn-0006LO-FL; Fri, 20 Jan 2023 03:59:05 -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 1pInEm-0006LF-7S for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:04 -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 1pInEl-0003T8-Ou for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pInEl-0004qr-EF for guix-patches@gnu.org; Fri, 20 Jan 2023 03:59:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60958] [PATCH 2/2] gnu: Add r-scds. 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Fri, 20 Jan 2023 09:58:11 +0100 From: Navid Afkhami Date: Fri, 20 Jan 2023 09:58:00 +0100 Message-ID: <20230120085800.47650-2-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230120085800.47650-1-navid.afkhami@mdc-berlin.de> References: <20230120085800.47650-1-navid.afkhami@mdc-berlin.de> 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--4.285300-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCQgqYHjJNWHeCZa9cSpBObnAuQ0xDMaXkH4q tYI9sRE/GXVOModIZ6bQQxIbVlM8FcocsHMOi3Ola87CDXaKRVJITEcvqjcF4EJZ5MDd4/kUU9a 6zfLFA1ZiaViLATk6nRf6uqcdjTP5oMIms1T5lV6ZAbAtg0x8FGVHNkCQpEYNxMMaN8PEwMHizy 75l6H5qX0tCKdnhB581kTfEkyaZdz6C0ePs7A07ba607moR85R/81B7MnSO+FU5O6Jlz3CkvVhF mLs9qk+JV8g6L21K9Pv6w6RwEMgdNMiqxyMWaBwOCQZAWK6OxJMGCPsxoOCn4HdimrhU7QidAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.285300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27396.006 X-TM-SNTS-SMTP: AA454C3E7DE36CD2CCD0527F9DEAC51B25E9F3D6462FF22FFD9BEA91DF7D26812002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -33 X-Spam_score: -3.4 X-Spam_bar: --- X-Spam_report: (-3.4 / 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, FUZZY_WALLET=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-scds): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 2 +- 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93c6165b62..bdbdeecc35 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet +;;; Copyright © 2023 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; @@ -7678,6 +7679,33 @@ (define-public r-trajectoryutils structures to hold pseudotime inference results.") (license license:gpl3))) +(define-public r-scds + (package + (name "r-scds") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scds" version)) + (sha256 + (base32 + "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + (properties `((upstream-name . "scds"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-matrix + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scds") + (synopsis "In-silico doublet annotation for single cell RNA sequencing data") + (description + "This is an R package for doublet annotation of single cell RNA sequencing data. +@code{scds} provides methods to annotate doublets in scRNA-seq data computationally.") + (license license:expat))) + (define-public r-slingshot (package (name "r-slingshot") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 86d65d2031..70ac252a8c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,7 +23,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2021 Felix Gruber -;;; Copyright © 2022 Navid Afkhami +;;; Copyright © 2022,2023 Navid Afkhami ;;; Copyright © 2022 Antero Mejr ;;; ;;; This file is part of GNU Guix.