From patchwork Fri Apr 8 14:59:52 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 38416 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 A35A327BBEA; Fri, 8 Apr 2022 16:09:12 +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_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, 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 6DC9727BBE9 for ; Fri, 8 Apr 2022 16:09:12 +0100 (BST) Received: from localhost ([::1]:60050 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ncqEZ-0007ch-I4 for patchwork@mira.cbaines.net; Fri, 08 Apr 2022 11:09:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53216) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0008TJ-Ch for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41660) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ncq6f-0001Wr-Mg for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ncq6f-0006Xh-LN for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54790] [PATCH 1/3] gnu: Add r-paralleldist. References: <20220408145829.3344728-1-zimon.toutoune@gmail.com> In-Reply-To: <20220408145829.3344728-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 08 Apr 2022 15:01:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54790@debbugs.gnu.org Cc: zimoun Received: via spool by 54790-submit@debbugs.gnu.org id=B54790.164943001225063 (code B ref 54790); Fri, 08 Apr 2022 15:01:01 +0000 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:12 +0000 Received: from localhost ([127.0.0.1]:35553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5r-0006W9-LN for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:11 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:42922) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5p-0006Ug-Hw for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f51.google.com with SMTP id r13so13257688wrr.9 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=yzSxJllHckq113wn6zoibfSTGdkE/qY7tXbbvW9Qsnw=; b=mXr9lyUTjsHrVjxNEa1R+7M9tNBNSy+RM6/jp1f3x8o9filazchHzkePupTyHpPu0W Atz4WUYL1epCgL6IohjwvO0vHob4n73oZAE8pkctZfD34Ss/oUNDsPHVTlfoLzy9i0R4 YqekfeCs5xm+aAc7Ex9F4KjcW8/4esFfCjqSkBjp3ptQOgMr1JTvWIM9/fAhJTv3ovpz +TI9WSauZN6U/wS3nALGT3g5a4DRFoZ5MPA91cwzYPdVFt6rg+Wfk4r7rZLodAuEY8bm fNX8jARx8UcoZM34MESnPQyn43TgURwP+IIPuSPcofcsHW3DsoMvwmJMKXvF5NxcD2/m OzTg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=yzSxJllHckq113wn6zoibfSTGdkE/qY7tXbbvW9Qsnw=; b=DY8U5QZJca7S+Rg5aCB9GaBkAtwLSbnmobE0LX/XUqv4s68IWRWYMeph39x80/5aZs bo8SArE42ZuuxwiiNYRu4t0MAYy8LYxfy4/UzQx1DLDu7FkqHQH6tvcy44ndHB8CuIN8 WI7o+WnSChSO6bPNxqjG3ai8slfxC50y8YJe5PKWbYGwONsHgxSFXMpQDRXUbN9yR3TJ a8opoWTk7rTPjfuTlww7p/vWTDW1JEJMicc1yS7Hk1RvYVhZZE5P86ZkgeDI4KZVMKVZ dYWQIQ5JZ15AzMQKaw5BOqJMKvIzTTXWN+xiXTQFVhiHxo3g7fPIcx1rx3rDfynLvS4d qNvQ== X-Gm-Message-State: AOAM533oVZnnwJK1NOqFlpm0DrG1k55G6QqzN77LLai8n/osF6CMpvFN onPkd0aCDpEoKQU6wV3RghKHQPpk/x8= X-Google-Smtp-Source: ABdhPJxfLkEXx61f5VHCQXbPtHzpveQ2o0oc8ENxjWi637MqTjtCZe8sCZ31bZnkkXNEK22+CzDDBg== X-Received: by 2002:a05:6000:1f9a:b0:207:9ad9:e300 with SMTP id bw26-20020a0560001f9a00b002079ad9e300mr1410346wrb.562.1649430003494; Fri, 08 Apr 2022 08:00:03 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:02 -0700 (PDT) From: zimoun Date: Fri, 8 Apr 2022 16:59:52 +0200 Message-Id: <20220408145954.3345224-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 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-paralleldist): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be77a57f28..b9ea1144f2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1074,6 +1074,39 @@ (define-public r-pacman functions which can speed up workflow.") (license license:gpl2))) +(define-public r-paralleldist + (package + (name "r-paralleldist") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "parallelDist" version)) + (sha256 + (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih")))) + (properties `((upstream-name . "parallelDist"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel)) + (home-page "https://github.com/alexeckert/parallelDist") + (synopsis "Parallel Distance Matrix Computation using Multiple Threads") + (description + "This package provides a fast parallelized alternative to R's native +'dist' function to calculate distance matrices for continuous, binary, and +multi-dimensional input matrices, which supports a broad variety of 41 +predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, +as well as user- defined functions written in C++. For ease of use, the +'parDist' function extends the signature of the 'dist' function and uses the +same parameter naming conventions as distance methods of existing R packages. +The package is mainly implemented in C++ and leverages the 'RcppParallel' +package to parallelize the distance computations with the help of the +'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is +used for optimized matrix operations during distance calculations. The +curiously recurring template pattern (CRTP) technique is applied to avoid +virtual functions, which improves the Dynamic Time Warping calculations while +the implementation stays flexible enough to support different DTW step +patterns and normalization methods.") + (license license:gpl2+))) + (define-public r-pheatmap (package (name "r-pheatmap") From patchwork Fri Apr 8 14:59:53 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 38414 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 B93B827BBE9; Fri, 8 Apr 2022 16:01:23 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,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 4765327BBEA for ; Fri, 8 Apr 2022 16:01:23 +0100 (BST) Received: from localhost ([::1]:49480 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ncq70-0008UB-Cp for patchwork@mira.cbaines.net; Fri, 08 Apr 2022 11:01:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53218) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0008TK-Cc for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41661) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0001Ws-26 for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ncq6g-0006Xp-1K for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54790] [PATCH 2/3] gnu: Add r-dlm. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 08 Apr 2022 15:01:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54790@debbugs.gnu.org Cc: zimoun Received: via spool by 54790-submit@debbugs.gnu.org id=B54790.164943001225072 (code B ref 54790); Fri, 08 Apr 2022 15:01:01 +0000 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:12 +0000 Received: from localhost ([127.0.0.1]:35555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5r-0006WC-V7 for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:12 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:44908) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5q-0006Uh-2D for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f41.google.com with SMTP id b19so13248636wrh.11 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=QezaVBJFJaEsjN0toj/LUr+drqv+xCkYVufm827opvk=; b=RvvlglJtyUngTErur3ESvRJbpWGITfLooFI2i5CiZ3Hd3oHMuVULjY03Wghjb4dlKl xxcBrx4xsJtAMriBZnTTj0Q7JEf5P+tUumjDS+f1cGFH01uFU8KhLWg+Vz1pZZmLzcAm y/oixUn1vD86OY3OTqyySLLzAi6+IV95+36AAakGY8qq0FWavXIuL7oPQQvzQNJdm3g6 MioeNsFzsvTGL3KUGJcN8dXmBcAmW1j4itfs7x8cBTJVZJd49HKkhVVS0PmyECJatFTG 5zu9xlIhm5TIPQS0rGOks/0kTysVGS4NGFYOCwpbSRlu7kQb4TmZjsc0xZ61T5dsVcj/ GBUQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=QezaVBJFJaEsjN0toj/LUr+drqv+xCkYVufm827opvk=; b=4O/fWm6iFFGwoqRRSy/Uw4NyPX2+XD98492gDLfOwKxv9tHLrzVKYX4HAGeEJjL6wS LxcmM9Ig/ia4a00pmj2CZJBE1U8mMCZM63aniSpVZSpt0hnBSa8PqfDRQfU44Nzjwo8b HRUyhrBr7eqj0LGRULL4rihCnZnd8sQWyvJ4ezjkObOzEnTiyaQv4++HMCCi9vXiQ+7+ 7g3SVdTF8QEXBrBQae4q/VK/daae+l4hjo63zeSA6XNbBj7GuxHPrYzn065c0QZLwHrl OM5maaBU33vVHf6sIVJzjqcXaPO8UL4Nuiqi+kHDisYW5D+xrIS932CVhYI1QwSSwHnh /Ejg== X-Gm-Message-State: AOAM533kToA9QvnCg7fWlmnr/01aSTIt/OK4MqeTTtwHmg4/JxFjuzpg ZxtaYsaP2V3QWEUVNr42lANZTxnttK8= X-Google-Smtp-Source: ABdhPJyagBXrGPpU7eJmBUKBUwQYiXQsCUEbDiSAKIbmHqecLn7KPqrS0ApQUyyw7vao2TNnF7Q+dg== X-Received: by 2002:a5d:6205:0:b0:1e4:b3fd:9ba8 with SMTP id y5-20020a5d6205000000b001e4b3fd9ba8mr14924471wru.426.1649430004161; Fri, 08 Apr 2022 08:00:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:03 -0700 (PDT) From: zimoun Date: Fri, 8 Apr 2022 16:59:53 +0200 Message-Id: <20220408145954.3345224-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220408145954.3345224-1-zimon.toutoune@gmail.com> References: <20220408145954.3345224-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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-dlm): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b9ea1144f2..5a852af4b7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -659,6 +659,26 @@ (define-public r-clipr the system clipboards.") (license license:gpl3))) +(define-public r-dlm + (package + (name "r-dlm") + (version "1.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "dlm" version)) + (sha256 + (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r")))) + (properties `((upstream-name . "dlm"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dlm") + (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models") + (description + "This package provides routines for Maximum likelihood, Kalman filtering +and smoothing, and Bayesian analysis of Normal linear State Space models, also +known as Dynamic Linear Models.") + (license license:gpl2+))) + (define-public r-zoo (package (name "r-zoo") From patchwork Fri Apr 8 14:59:54 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 38415 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 E1A7E27BBEA; Fri, 8 Apr 2022 16:01:24 +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_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, 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 AFF0A27BBE9 for ; Fri, 8 Apr 2022 16:01:24 +0100 (BST) Received: from localhost ([::1]:49520 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ncq71-0008WD-Pi for patchwork@mira.cbaines.net; Fri, 08 Apr 2022 11:01:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53220) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0008Tf-NZ for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41662) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0001X3-EU for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ncq6g-0006Xw-Dl for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54790] [PATCH 3/3] gnu: Add r-copykat. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 08 Apr 2022 15:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54790@debbugs.gnu.org Cc: zimoun Received: via spool by 54790-submit@debbugs.gnu.org id=B54790.164943001325079 (code B ref 54790); Fri, 08 Apr 2022 15:01:02 +0000 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:13 +0000 Received: from localhost ([127.0.0.1]:35557 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5s-0006WL-DM for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:12 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:44910) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5q-0006Uj-BP for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f42.google.com with SMTP id b19so13248659wrh.11 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=j+hXwvUXMbaWqOMo9lk/3RpKHTxFGBAK6Qgf5aVGuG55YXHtYcj1rPPJnxw3G2CTc9 kzmhaP82A9kUDpt+ycR5K3gIGoaZ4S5bMExQ0TyWHdGnY3uFEngdf3Pe5l0gptz04rs9 is7c/29hD3nduBHVCfwuJX2kIO/aBKgnKyGrUoLUQLVdR8c9T3+aIsJzUdrXDJMxLZL5 UqMuzXTHO8MIKySkL7vR2Vep9EjRNWQtnj+agcQu6B9EXUzqm3MiHSSS3YUzr8XYXZn5 NVYBt/h1BQTJGsVzqbT7cMhEf0k+AR9aNVfeYjvRYfvXgMV1pMTQLKWAhD0wEuHny9eO Be/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=SDyZg2UeBrb2Aw3VqAjSybZRGDWEpk+uRmL5H6nI7w3yjJZZCprw1ey+/VXGBk8666 iAe+u+b8t838nNu7+RafXbsZ+RK5XfySzKoR2dmrhO2bR3ZMHh35r7TntbSVLZRUHIbE KB66h7tBP0Gq2c9/rD3M2fSXg5k8atDkVKXJyzX+FfB2+LwekxZKT0e4Y1573RJzMRdo LNuq+eG8E4fbQYaBC8T7sPo57MySvM15tU8uRfy5V4cTQ8SNrZE/zi4eMdwMWfZbn2c3 3kT5tlYj7+aCAsuvnDWxZ6e/sUwhZAKe89HxIX8a7o4X0Y+j+xLEFaqdjkGwviVOPO9S UMRg== X-Gm-Message-State: AOAM533BbYUTY7KgK6q5dK8aCYmfV2i+w8QdQdEqlhTOapVulbr7c9Uu 27MQ7xzV+R1L0QiORUS1udDUbW5MCwU= X-Google-Smtp-Source: ABdhPJx5iq4zn1R8NiglR4QyX0bQTdvRTeWZ7Q7d+l8vfiC3g8YsoAZO9Dmo+P3/K7LP5i2wXR1V5Q== X-Received: by 2002:a05:6000:18c3:b0:206:1575:ec8f with SMTP id w3-20020a05600018c300b002061575ec8fmr14565176wrq.479.1649430004653; Fri, 08 Apr 2022 08:00:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:04 -0700 (PDT) From: zimoun Date: Fri, 8 Apr 2022 16:59:54 +0200 Message-Id: <20220408145954.3345224-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220408145954.3345224-1-zimon.toutoune@gmail.com> References: <20220408145954.3345224-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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/bioinformatics.scm (r-copykat): New variable. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 106b25a50b..e3cca9aab8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9138,6 +9138,44 @@ (define-public r-cellchat communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba")