From patchwork Fri Feb 3 12:18:52 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46630 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 627A727BBED; Fri, 3 Feb 2023 12:20:21 +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 6F68D27BBE9 for ; Fri, 3 Feb 2023 12:20:20 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNv30-0005l9-CC; Fri, 03 Feb 2023 07:20:07 -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 1pNv2w-0005id-Dy for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -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 1pNv2w-0005vi-1B for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNv2v-0001JP-N2 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61250] [PATCH 1/3] gnu: Add r-viper. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Feb 2023 12:20:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61250 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61250@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16754267694963 (code B ref -1); Fri, 03 Feb 2023 12:20:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:29 +0000 Received: from localhost ([127.0.0.1]:36658 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2O-0001Hu-I6 for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:28 -0500 Received: from lists.gnu.org ([209.51.188.17]:39724) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2M-0001Hk-2Q for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:27 -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 1pNv2K-0005Xk-JR for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -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 1pNv2I-0005p5-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -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=1675426749; x=1677241150; bh=yXMCYYaKRkcpM8P enon+bzc41XnrJnjp7pfBmpmFWWs=; b=AwxynC8ZP7d0gm/Oj6WWloOYhGMeVXA /3ai8pdLSw71LinqK1LLvlmHWeUtTc4xNWVbEWAi76XLaAW48T7DlocPcwLaoOkK z9pwFd3FFiuZbO0kjYaIXDt2VjS6W2ixdy+DS0P4JHxHNNJZ9g2vSi1BBLMT2qU3 4wJ3CQtISYEw= 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 2205F30046A for ; Fri, 3 Feb 2023 13:19:06 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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, 3 Feb 2023 13:19:05 +0100 From: Navid Afkhami Date: Fri, 3 Feb 2023 13:18:52 +0100 Message-ID: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [10.84.128.45] 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-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10-2.372600-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEMwD q5LCkpMyRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9AKgfO6jacGaY5ZGw7wyeHvSr X73EbCvzF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2Klf+gmVy5VdZkmfrd mIETRVJ87q+UfprFy0Z/QAh+OcADEdfRFpwHjBvzmcRWGv0Z11+KPePv/jwUtPGwBtlzRKvdyNs TVQr6HGarvaEx2RCcooQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.372600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: C8F6CBFBE2B4DB989EA6D0CD98E8BBCE891A3EAA3FAAA7DAEB1AA67237822D292002: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/bioconductor.scm (r-viper): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 711b988e7f..aeef6f4106 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8307,6 +8307,27 @@ (define-public r-variantannotation coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-viper + (package + (name "r-viper") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "viper" version)) + (sha256 + (base32 + "11i2q9nakh534nx2l736id7k1yqhk7jpg32sbfl4vrnh398q86h6")))) + (properties `((upstream-name . "viper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071 r-kernsmooth r-mixtools)) + (home-page "https://bioconductor.org/packages/viper") + (synopsis + "Virtual inference of protein-activity by enriched regulon analysis") + (description + "Inference of protein activity from gene expression data. +Including the VIPER and msVIPER algorithms") + (license license:gpl2+))) + (define-public r-vsn (package (name "r-vsn") From patchwork Fri Feb 3 12:18:53 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46631 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 B090E27BBE9; Fri, 3 Feb 2023 12:20:44 +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 5FEF427BBF0 for ; Fri, 3 Feb 2023 12:20:40 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNv32-0005m7-G4; Fri, 03 Feb 2023 07:20:08 -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 1pNv2w-0005jf-RS for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -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 1pNv2w-0005yL-G4 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNv2w-0001Je-9V for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61251] [PATCH 2/3] gnu: Add r-bcellviper. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Feb 2023 12:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61251 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61251@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16754267694970 (code B ref -1); Fri, 03 Feb 2023 12:20:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:29 +0000 Received: from localhost ([127.0.0.1]:36660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2O-0001I5-VG for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:29 -0500 Received: from lists.gnu.org ([209.51.188.17]:39730) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2O-0001Hm-8i for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:28 -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 1pNv2K-0005Xj-JB for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -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 1pNv2I-0005p8-9P for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1675426750; x=1677241151; bh=IzOPx4wThypuvHqyxfAHTEoBHsxmomtjeKTe91Xxwm4=; b=C1MhILLpRDpW 3j9YRnCbehIicnQ8tQmzKtWemkOuK6jTFoZT90DcNwcuBHtn2FTYOYhdzcBwQLkP 6+FWAsClInhMq0N/LWnFyb6ow6kAqwO06URCsh107JPstHiGJ1EDPDed7WpT1R1o YosxskkHqspJuU0BB+aaLwmLeGWvDQg= 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 6F00B300471 for ; Fri, 3 Feb 2023 13:19:10 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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, 3 Feb 2023 13:19:05 +0100 From: Navid Afkhami Date: Fri, 3 Feb 2023 13:18:53 +0100 Message-ID: <20230203121854.95308-2-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> References: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [10.84.128.45] 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-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10--4.310400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkENBi hTOKX++2RRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRlFexdJHJX6CepM qtPiQJGkigvsxCV7yoXPF44cFsZvM0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSk6XE E7Yhw4FqEyPuTWsskax2siDKQnB+391IkCwx8EmS2Z6HhmRFk1+CQPx05nlQjrfam4l6XNJzZoi x8YAtS5yCTT9C8fWkqnjH/1auG6Ot8iatREjfpDE8nb9DwdQ4C2jbSab1pg0UjxFpwn53SOfhj5 CZkmSyI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.310400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: 542675C4D8BF71FA0DB670CCD57B2CAA75ACF4973867B06E80D415563DE5FEA32002: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/bioconductor.scm (r-bcellviper): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aeef6f4106..521d6c00be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1248,6 +1248,29 @@ (define-public r-arrmdata from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-bcellviper + (package + (name "r-bcellviper") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bcellViper" version + 'experiment)) + (sha256 + (base32 + "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm")))) + (properties `((upstream-name . "bcellViper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/bcellViper") + (synopsis + "Transcriptional interactome and normal human B-cell expression data") + (description + "This is a tool for human B-cell context-specific transcriptional regulatory network. +In addition, this package provides a human normal B-cells dataset for +the examples in package viper.") + (license license:gpl2+))) + (define-public r-bladderbatch (package (name "r-bladderbatch") From patchwork Fri Feb 3 12:18:54 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46632 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 0354D27BBED; Fri, 3 Feb 2023 12:20:53 +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 4012A27BBE9 for ; Fri, 3 Feb 2023 12:20:52 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNv2y-0005kq-M0; Fri, 03 Feb 2023 07:20:04 -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 1pNv2x-0005kV-9M for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:03 -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 1pNv2w-0005zw-Vt for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNv2w-0001Js-Qi for guix-patches@gnu.org; Fri, 03 Feb 2023 07:20:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61252] [PATCH 3/3] gnu: Add r-dorothea. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Feb 2023 12:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61252 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61252@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16754267724986 (code B ref -1); Fri, 03 Feb 2023 12:20:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:32 +0000 Received: from localhost ([127.0.0.1]:36663 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2S-0001IM-Ax for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:32 -0500 Received: from lists.gnu.org ([209.51.188.17]:39742) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2Q-0001ID-7B for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:31 -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 1pNv2L-0005Xu-Uo for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:26 -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 1pNv2I-0005pD-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:25 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1675426751; x=1677241152; bh=8gMs13RjcFm7Ib7dhV+P1XLIuucG7EinnFOA2S1dWSY=; b=U6PSnHFsQO8d lSSCX//TM25JkGQT4gTFjfD8MVQalEksK4RKxEPhHl2vR0TcYxytubxoqg2rHpGF t/Jsp3HbFhuOazBrTPjtMeoV/u/3jZHqn4VQz7V59H4297xUoXYZKLByTV7RlQid 0nYJMqQ1KMldrnzjHG0mGBcLDNPPcsk= 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 2D2DD300476 for ; Fri, 3 Feb 2023 13:19:11 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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, 3 Feb 2023 13:19:06 +0100 From: Navid Afkhami Date: Fri, 3 Feb 2023 13:18:54 +0100 Message-ID: <20230203121854.95308-3-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> References: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [10.84.128.45] 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-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10--5.692400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57MXjfR3d0weRpQOYBrXJCKAWFC ZbvPiXUWOpcUW0o8+sKD8el0BdzuolAEOTWU7+ZWrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGij+ffe3B1tiAu8sKJSXbINbwjHXliV4XMOSR1u+6Od8u1AJBZ5UxqA= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.692400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: 22E8D98D8E5D3F45818B6CDCE81E41EB190CE94F0116AEE689D110AC5F7CCD282002: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/bioconductor.scm (r-dorothea): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 521d6c00be..0786160b5e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -466,6 +466,31 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10 in Biostrings objects.") (license license:artistic2.0))) +(define-public r-dorothea + (package + (name "r-dorothea") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dorothea" version + 'experiment)) + (sha256 + (base32 + "05vkb5mash2m8p6njk842sy5pz7vblrm8n9bphqbslm86kld5n92")))) + (properties `((upstream-name . "dorothea"))) + (build-system r-build-system) + (propagated-inputs (list r-bcellviper r-dplyr r-magrittr r-viper)) + (native-inputs (list r-knitr)) + (home-page "https://saezlab.github.io/dorothea/") + (synopsis "Collection of human and mouse TF regulons") + (description + "DoRothEA is a gene regulatory network containing signed transcription factor. +DoRothEA regulons, the collection of a TF andits transcriptional targets, +were curated and collected from different types ofevidence for both human +and mouse. A confidence level was assigned to each TF-target interaction +based on the number of supporting evidence.") + (license license:gpl3))) + (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata")