From patchwork Thu Aug 24 13:28:27 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 53192 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 8665A27BBE9; Thu, 24 Aug 2023 14:29:11 +0100 (BST) 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,MAILING_LIST_MULTI,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 C075127BBE2 for ; Thu, 24 Aug 2023 14:29:08 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qZAOV-0004wU-I7; Thu, 24 Aug 2023 09:29:03 -0400 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 1qZAOQ-0004tZ-Nq for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:59 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qZAOQ-0004K6-Fl for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:58 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qZAOU-0005n2-EX for guix-patches@gnu.org; Thu, 24 Aug 2023 09:29:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 Aug 2023 13:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 65499 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65499@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169288373422237 (code B ref -1); Thu, 24 Aug 2023 13:29:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:28:54 +0000 Received: from localhost ([127.0.0.1]:36380 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOM-0005ma-7f for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:54 -0400 Received: from lists.gnu.org ([2001:470:142::17]:38558) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOK-0005mN-BX for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:53 -0400 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 1qZAOA-0004cQ-Ar for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -0400 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 1qZAO7-0004H4-IE for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -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=1692883711; x=1694698112; bh=2uKKU06f9iIOnwP WPN/bQneLN+rbCL4mIuhymLP0yiM=; b=G5XjZ5dQw0VkYSuiX4NRUHerbPBbs51 4XICsaM+EElrDoZeWqKoQ16AuNO2zv5ztsAhpKAa8/pfnL6wlAPjVDQEI8qFS57G yJTWcJCAmOWa0fRvr1/U5B3n950BrCGl/qNw3T6fOkIgOk9ckYFPNdcMoTfZByeg cjQxtOUIjPiw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DF4B7A02C9 for ; Thu, 24 Aug 2023 15:28:31 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Thu, 24 Aug 2023 15:28:31 +0200 From: Navid Afkhami Date: Thu, 24 Aug 2023 13:28:27 +0000 Message-ID: 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-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--6.678300-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNTZ+DFCYZ6Lz/b Pm7tO5sURRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9pkBMYDn8FeK9j7aNnpjtlmUD gikHuA07Ga3MOTq0sPzOU0DmKJatfWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+6vV BUUydJCsRB0bsfrpPIFT1PBs+MVY3yU/oX+tpNmMNemkBN1aNy9gwOgJ18nxkwHwLpmah7BmhxU vc1FhawdNLEhCSvfmMchXTZ3Wukbw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.678300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F0A08225987C4BD0F992713D7159E1354A35F1F337329C02E363CA25C1974DF82000: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-bumpymatrix): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) base-commit: 39fa1ef033fda82cb1d122e0d1675b51acb1db34 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74071900a3..6204173277 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12913,6 +12913,33 @@ (define-public r-siggenes Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) +(define-public r-bumpymatrix + (package + (name "r-bumpymatrix") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BumpyMatrix" version)) + (sha256 + (base32 + "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i")))) + (properties `((upstream-name . "BumpyMatrix"))) + (build-system r-build-system) + (propagated-inputs (list r-iranges r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BumpyMatrix") + (synopsis "Bumpy matrix of non-scalar objects") + (description + " +@code{BumpyMatrix} class and subclasses for storing non-scalar objects in matrix entries. +This is akin to a ragged array but the raggedness is in the third dimension, +much like a bumpy surface - hence the name. Of particular interest is the +@code{BumpyDataFrameMatrix,} where each entry is a Bioconductor data frame. +This allows us to naturally represent multivariate data in a format that is +compatible with two-dimensional containers like the @code{SummarizedExperiment} +and @code{MultiAssayExperiment} objects.") + (license license:expat))) + (define-public r-bumphunter (package (name "r-bumphunter") From patchwork Thu Aug 24 13:28:28 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 53193 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 BFA2C27BBEA; Thu, 24 Aug 2023 14:30:17 +0100 (BST) 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,MAILING_LIST_MULTI,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 DD92E27BBE2 for ; Thu, 24 Aug 2023 14:30:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qZAPQ-0005gr-P3; Thu, 24 Aug 2023 09:30:00 -0400 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 1qZAPP-0005gb-BT for guix-patches@gnu.org; Thu, 24 Aug 2023 09:29:59 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qZAPP-0004Ox-3C for guix-patches@gnu.org; Thu, 24 Aug 2023 09:29:59 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qZAPT-0005p7-1c for guix-patches@gnu.org; Thu, 24 Aug 2023 09:30:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 Aug 2023 13:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 65500 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65500@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169288374522283 (code B ref -1); Thu, 24 Aug 2023 13:30:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:29:05 +0000 Received: from localhost ([127.0.0.1]:36385 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOW-0005nL-Mn for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:05 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55966) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOU-0005mm-Hq for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:03 -0400 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 1qZAOI-0004ss-BP for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:51 -0400 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 1qZAOF-0004Hf-Oc for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:50 -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=1692883724; x=1694698125; bh=cLOAy6V9r7ftjSfWBlwGYV1T6bdUteTp5LMhsPgw1Ug=; b=l42BNeKz74E/ QVI68gSSRlJr/dBqm1KTJN3doDUbF1Z2ht3EHR1c9+TrZV2YcMuwvHTGrqQ56LUt E4osRMKWHpC6PWtjXCQYp21CIq3S5f2YkkDFKFlRtMgoAtcssEgktuQme9N9K+z3 73BPAxAPbpd9YSQWLMP8hZldQBlDzPo= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id CC5F616034E for ; Thu, 24 Aug 2023 15:28:44 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Thu, 24 Aug 2023 15:28:44 +0200 From: Navid Afkhami Date: Thu, 24 Aug 2023 13:28:28 +0000 Message-ID: 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-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--3.113400-5.000000 X-TMASE-MatchedRID: JUGAxiLh1cP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZL9Yv7P2J5iwmA0 yITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUdARBOrTIjN2Y4wgQ05hcUMzww 9tSb2RaGR2/d8xMND2Xzt7UAp5umA2DUaxs6FR5E7JKKPALJUtfBs3rZsh/GcXAvh586il4W/H7 LhIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.113400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F18E0FDAC4FAF4C20F649067E2E4CF8EFC7A36BCDD5A6048498EACB72457B7ED2000: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/bioconductor.scm (r-mousegastrulationdata): 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 6204173277..f3671e5cca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8009,6 +8009,37 @@ (define-public r-motifrg throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mousegastrulationdata + (package + (name "r-mousegastrulationdata") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MouseGastrulationData" version + 'experiment)) + (sha256 + (base32 + "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17")))) + (properties `((upstream-name . "MouseGastrulationData"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-bumpymatrix + r-experimenthub + r-s4vectors + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/MarioniLab/MouseGastrulationData") + (synopsis + "Single-Cell omics data across mouse gastrulation and early organogenesis") + (description + "This package provides processed and raw count data for single-cell RNA sequencing. +in addition, this package offers single-cell ATAC-seq, and @code{seqFISH} +(spatial transcriptomic) experiments performed along a timecourse of mouse +gastrulation and early organogenesis.") + (license license:gpl3))) + (define-public r-muscat (package (name "r-muscat")