From patchwork Tue May 3 06:53:08 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 39092 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 5586227BBEA; Tue, 3 May 2022 07:55:23 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 C858F27BBE9 for ; Tue, 3 May 2022 07:55:22 +0100 (BST) Received: from localhost ([::1]:37002 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nlmRN-0000U9-VI for patchwork@mira.cbaines.net; Tue, 03 May 2022 02:55:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47892) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmQD-00004q-NC for guix-patches@gnu.org; Tue, 03 May 2022 02:54:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44645) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nlmQ6-0006hE-Ff for guix-patches@gnu.org; Tue, 03 May 2022 02:54:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nlmQ6-00061X-Eb for guix-patches@gnu.org; Tue, 03 May 2022 02:54:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55239] [PATCH 1/4] gnu: Add r-forestplot. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 03 May 2022 06:54:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 55239 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55239@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.165156081123069 (code B ref -1); Tue, 03 May 2022 06:54:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 May 2022 06:53:31 +0000 Received: from localhost ([127.0.0.1]:38534 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nlmPa-0005zw-TT for submit@debbugs.gnu.org; Tue, 03 May 2022 02:53:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:45494) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nlmPY-0005zg-W5 for submit@debbugs.gnu.org; Tue, 03 May 2022 02:53:29 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47842) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmPY-0008Mb-MV for guix-patches@gnu.org; Tue, 03 May 2022 02:53:28 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54845) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmPW-0006ev-Pl for guix-patches@gnu.org; Tue, 03 May 2022 02:53:28 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id E6BE7300150 for ; Tue, 3 May 2022 08:53:24 +0200 (CEST) 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:received:received; s=mdc; t=1651560804; x=1653375205; bh=qy+s91X9rSp3O9FbFQoMxNNSBlOMV7cj8xmdlakeVwA=; b=j15B9MJjWPTh sHQIuLFv+4525p3BKysqhvJEpjiBh6vM4O/uEr/ZlymdoqIs4/WARGzQZ9MxoHtF 3JxeSQDRAPaK3JHP8Qh6dr2ODIy/jSWFY23dp92oLDaXvtabvVTm0SE3+xakqZ/I 1oXfqFR+XWlG2fvs5E/vBnXmMCL0MrM= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id fFyXvrNb5btI for ; Tue, 3 May 2022 08:53:24 +0200 (CEST) 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 for ; Tue, 3 May 2022 08:53:24 +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 15.1.2507.6; Tue, 3 May 2022 08:53:23 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 3 May 2022 08:53:08 +0200 Message-ID: <20220503065311.9192-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26870.006 X-TM-AS-Result: No-10--4.218400-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCStPpXoicS5XwTlc9CcHMZerwqxtE531VICu qghmtWfXxUae82fvOzup9XBHPjLuGiq+GZ9ZHxIhuW77/y896siFzNNPDc6umMicqvB+icULi0x TsP0eePJ7MSP7SLpuGHpRFDEAszMOx7fBXoDaFyFFdmLrX42PXAT2OEnoCt4864sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJcFwgTvxipFa9xS3mVzWUuBHZpq/WXaosp47i FwVw1xCR/xVHeito/YRzMLiflNVaC44DBqyWdXNV6fpQuk3VQiNac/lldi2V/YZmkLT0MpvX5Dy SDQYgp8xlBL5DyzlmdxSR7be7fnTFTs4ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.218400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26870.006 X-TM-SNTS-SMTP: B97AFE3C31843BA4AA5EC07B55653CFCDF8D1F93183509469F62A5668AFD22B12002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 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/cran.scm (r-forestplot): New variable. X-Debbugs-Cc: rekado@elephly.net --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) base-commit: 098f2eea331121905e3c867f478b22cea3510841 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 91c54bac9a..864540adf1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24377,6 +24377,33 @@ (define-public r-forecast space models and automatic ARIMA modelling.") (license license:gpl3))) +(define-public r-forestplot + (package + (name "r-forestplot") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "forestplot" version)) + (sha256 + (base32 + "0bzwi6ws0qjq1pqiadssynbkxxd4zjp974jfdplmv16fcyszqhyi")))) + (properties `((upstream-name . "forestplot"))) + (build-system r-build-system) + (propagated-inputs + (list r-checkmate + r-magrittr)) + (native-inputs (list r-knitr)) + (home-page "https://gforge.se/packages/") + (synopsis "Advanced forest plot using @code{grid} graphics") + (description + "This package provides a forest plot that allows for multiple confidence +intervals per row, custom fonts for each text element, custom confidence +intervals, text mixed with expressions, and more. The aim is to extend the use +of forest plots beyond meta-analyses. This is a more general version of the +original @code{rmeta} package's @code{forestplot()} function and relies heavily +on the @code{grid} package.") + (license license:gpl2))) + (define-public r-formattable (package (name "r-formattable") From patchwork Tue May 3 06:53:09 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 39093 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 7903E27BBEA; Tue, 3 May 2022 07:55:48 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 0B30127BBE9 for ; Tue, 3 May 2022 07:55:48 +0100 (BST) Received: from localhost ([::1]:37252 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nlmRn-0000f3-88 for patchwork@mira.cbaines.net; Tue, 03 May 2022 02:55:47 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47890) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmQD-0008WV-NG for guix-patches@gnu.org; Tue, 03 May 2022 02:54:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44643) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nlmQ5-0006hB-T2 for guix-patches@gnu.org; Tue, 03 May 2022 02:54:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nlmQ5-00061J-Ru for guix-patches@gnu.org; Tue, 03 May 2022 02:54:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55238] [PATCH 2/4] gnu: Add r-catdata. 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envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 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/cran.scm (r-catdata): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 864540adf1..63e2b71cd3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8191,6 +8191,28 @@ (define-public r-catdap evaluated by the @dfn{Akaike Information Criterion} (AIC).") (license license:gpl2+))) +(define-public r-catdata + (package + (name "r-catdata") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (cran-uri "catdata" version)) + (sha256 + (base32 + "14kx7yi0cv6dyh9wjasb8gn6cp1bhglgwql7dc2a7lqvdcp0d5vj")))) + (properties `((upstream-name . "catdata"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://cran.r-project.org/package=catdata") + (synopsis + "Datasets and examples used in the book @emph{Regression for Categorical Data}") + (description + "This R package contains examples from the book @emph{Regression for +Categorical Data}, Tutz 2012, Cambridge University Press. The names of the +examples refer to the chapter and the data set that is used.") + (license license:gpl2))) + (define-public r-arules (package (name "r-arules") From patchwork Tue May 3 06:53:10 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 39091 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 7EA8527BBEA; Tue, 3 May 2022 07:55:16 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 1001F27BBE9 for ; Tue, 3 May 2022 07:55:16 +0100 (BST) Received: from localhost ([::1]:36632 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nlmRH-00008U-5t for patchwork@mira.cbaines.net; Tue, 03 May 2022 02:55:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47896) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmQD-00004r-OL for guix-patches@gnu.org; Tue, 03 May 2022 02:54:13 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44649) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nlmQ7-0006hG-M1 for guix-patches@gnu.org; Tue, 03 May 2022 02:54:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nlmQ7-000621-LM for guix-patches@gnu.org; Tue, 03 May 2022 02:54:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55241] [PATCH 3/4] gnu: Add r-smurf. 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envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 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/cran.scm (r-smurf): New variable. --- gnu/packages/cran.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 63e2b71cd3..099bfb8002 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5907,6 +5907,48 @@ (define-public r-sm and density estimation") (license license:gpl2+))) +(define-public r-smurf + (package + (name "r-smurf") + (version "1.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "smurf" version)) + (sha256 + (base32 + "00q54pg42anilhcshhjvv277mkszbpzpkf1g7srs7cjd5skjvsaf")))) + (properties `((upstream-name . "smurf"))) + (build-system r-build-system) + (propagated-inputs + (list r-catdata + r-glmnet + r-mass + r-matrix + r-mgcv + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-speedglm)) + (native-inputs (list r-knitr)) + (home-page "https://gitlab.com/TReynkens/smurf") + (synopsis "Sparse multi-type regularized feature modeling") + (description + "The @code{smurf} package contains the implementation of the @dfn{Sparse +Multi-type Regularized Feature} (SMuRF) modeling algorithm to fit +@dfn{generalized linear models} (GLMs) with multiple types of predictors via +regularized maximum likelihood. Next to the fitting procedure, following +functionality is available: + +@itemize @bullet +@item +Selection of the regularization tuning parameter lambda using three different +approaches: in-sample, out-of-sample or using cross-validation. +@item +S3 methods to handle the fitted object including visualization of the coefficients +and a model summary. +@end itemize") + (license license:gpl2+))) + (define-public r-venndiagram (package (name "r-venndiagram") From patchwork Tue May 3 06:53:11 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 39090 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 2B24E27BBEA; Tue, 3 May 2022 07:55:14 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 B02F227BBE9 for ; Tue, 3 May 2022 07:55:13 +0100 (BST) Received: from localhost ([::1]:36598 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nlmRE-00006t-Ra for patchwork@mira.cbaines.net; Tue, 03 May 2022 02:55:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47898) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nlmQD-00004s-OD for guix-patches@gnu.org; Tue, 03 May 2022 02:54:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44647) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nlmQ7-0006hF-3B for guix-patches@gnu.org; Tue, 03 May 2022 02:54:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nlmQ7-00061m-2B for guix-patches@gnu.org; Tue, 03 May 2022 02:54:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55240] [PATCH 4/4] gnu: Add r-airpart. 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envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 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-airpart): New variable. --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a78903becc..2967c5016b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1877,6 +1877,52 @@ (define-public r-agilp ;; GPLv3. (license license:gpl3))) +(define-public r-airpart + (package + (name "r-airpart") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "airpart" version)) + (sha256 + (base32 + "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06")))) + (properties `((upstream-name . "airpart"))) + (build-system r-build-system) + (propagated-inputs + (list r-apeglm + r-clue + r-complexheatmap + r-dplyr + r-dynamictreecut + r-emdbook + r-forestplot + r-ggplot2 + r-lpsolve + r-matrixstats + r-mclust + r-pbapply + r-plyr + r-rcolorbrewer + r-rlang + r-s4vectors + r-scater + r-singlecellexperiment + r-smurf + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/airpart") + (synopsis "Differential cell-type-specific allelic imbalance") + (description + "The @code{airpart} package identifies sets of genes displaying differential +cell-type-specific allelic imbalance across cell types or states, utilizing +single-cell allelic counts. It makes use of a generalized fused lasso with +binomial observations of allelic counts to partition cell types by their allelic +imbalance. Alternatively, a nonparametric method for partitioning cell types +is offered. The package includes a number of visualizations and quality control +functions for examining single cell allelic imbalance datasets.") + (license license:gpl2))) + (define-public r-aneufinder (package (name "r-aneufinder")