From unknown Sat Sep 06 00:52:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#56142] [PATCH] gnu: Add r-aseb. 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Wed, 22 Jun 2022 15:57:55 +0200 (CEST) Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 22 Jun 2022 15:57:55 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.9; Wed, 22 Jun 2022 15:57:54 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Wed, 22 Jun 2022 15:57:41 +0200 Message-ID: <20220622135741.16618-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-AS-Result: No-10-0.211700-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzFIcsAc8jehkqa6TyhyXvPbqL 7Fma/TB8hHr+pkQiTeJ+XXzWmAMTULmsVDuK2FjyQJOFc+qyqK83dpdHr49yZ64sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJShNCXvA0fw+jaPj0W1qn0TKayT/BQTiGqr9r fzj4GbEcReVTV/zMZmjvBzjRJE72EDr7D5ZwrlJM5L6Azz9MyNiSpMo2OO7ky6FyX3DDsVUxspd MdNUyuAv8O7hvDpIuy24H4xRId62tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfQ5+gyyDasGNDDKa 3G4nrLQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.211700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-SNTS-SMTP: D2ADA119C79201734F3C88B261FBE2BDF8D94596C1E2F626AA88167CFCB0A1E52002: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-Spam-Score: -1.4 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-aseb): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..f961d201d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,32 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-aseb + (package + (name "r-aseb") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASEB" version)) + (sha256 + (base32 + "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + (properties `((upstream-name . "ASEB"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/ASEB") + (synopsis "Predict acetylated lysine sites") + (description + "@code{ASEB} is an R package to predict lysine sites that can be acetylated +by a specific @dfn{KAT}-family (K-acetyl-transferases). Lysine acetylation is +a well-studied posttranslational modification on kinds of proteins. About four +thousand lysine acetylation sites and over 20 lysine KATs have been identified. +However, which KAT is responsible for a given protein or lysine site acetylation +is mostly unknown. In this package, we use a @dfn{GSEA}-like (Gene Set Enrichment +Analysis) method to make predictions. GSEA method was developed and successfully +used to detect coordinated expression changes and find the putative functions +of the long non-coding RNAs.") + (license license:gpl3+))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 From unknown Sat Sep 06 00:52:51 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#56142: closed ([PATCH] gnu: Add r-aseb.) Message-ID: References: <87sfj3bu2b.fsf@elephly.net> <20220622135741.16618-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 56142 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 56142@debbugs.gnu.org Date: Mon, 31 Oct 2022 20:47:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1667249222-6739-1" This is a multi-part message in MIME format... ------------=_1667249222-6739-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #56142: [PATCH] gnu: Add r-aseb. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 56142@debbugs.gnu.org. --=20 56142: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56142 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1667249222-6739-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 56142-done) by debbugs.gnu.org; 31 Oct 2022 20:46:11 +0000 Received: from localhost ([127.0.0.1]:42013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbff-0001jb-3A for submit@debbugs.gnu.org; Mon, 31 Oct 2022 16:46:11 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21159) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1opbfe-0001jS-0S for 56142-done@debbugs.gnu.org; Mon, 31 Oct 2022 16:46:10 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1667249168; cv=none; d=zohomail.com; s=zohoarc; b=VelxTva/shIS/+6MckXX9c7xCjejDZnUizfoDebBxvi//xm7JmlyoOcpgomsgq+LWmGOHG6jeggQsXeTzlwXqmprFifO5ASSbg+tSr2U6EC5Q6IJpYohD2NIorPDLPpYwQstepJTCV8rp/o8pOL2twYUf2kCH76ppzg41ENBP6g= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1667249168; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=hVHMWPhERWuZ6SA85KBIGpFDFa7oL4m9CwckuoCr93VgCjLHIUb+1XjjR7imDnZxJBDrks/vx+rAD5l9ROwjBfJYjz65bputctaS8zID9m/75v6rms3ZoNDo18mugMWi7xkAV5tV7RRnTz39G1QF0nq44AaHLzho61N8m+E0y4c= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1667249168; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=gdevwcMI/inxjqSbS8+VDKy4PHwXsCkfPB+HJFzDf9bzmgA3umMmiehIDxzkJE6R AXo+QimOckWrXPr8Pjsh8EDvxIIEmONhiiCEQdUB9vuu5Z+TB7RyXYOc4Iqx4HFwZq7 5sp22KuBiikqoK37xT65+OFkmOacEPYDQx3eBbBI= Received: from localhost (155-111-142-46.pool.kielnet.net [46.142.111.155]) by mx.zohomail.com with SMTPS id 1667249167073370.43340323959217; Mon, 31 Oct 2022 13:46:07 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56142-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-aseb. Date: Mon, 31 Oct 2022 21:45:47 +0100 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87sfj3bu2b.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 56142-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Applied, thanks! -- Ricardo ------------=_1667249222-6739-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 22 Jun 2022 13:58:16 +0000 Received: from localhost ([127.0.0.1]:36178 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40s4-0001xV-2N for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:58:16 -0400 Received: from lists.gnu.org ([209.51.188.17]:60128) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40rt-0001xC-8j for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:58:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51800) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40rr-0003jz-P4 for guix-patches@gnu.org; Wed, 22 Jun 2022 09:58:04 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:43039) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40rn-0000mo-Uv for guix-patches@gnu.org; Wed, 22 Jun 2022 09:58:02 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 1E4D730022E for ; Wed, 22 Jun 2022 15:57:56 +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=1655906275; x=1657720676; bh=EsGLgWaR23lEHJ97Sx3WjvUJcI+8XkL07Dv0muVB264=; b=PLIwjsQ9fOru +VKr+cT18z7EZwsW1+odxvcxGqyr3DsuxIawy21dnlJLHcir3Rh+lKpG+Cu6S2hD kJTZ0c/wSA8jb7vihIsl80CN+k25HB53vQULwMMIvl2o3O/k1DDfQOv86PbAsRjy IaT1EwS2G8vsKVz3e4rfTxX4wtJNtCA= 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 DOx5rSZWW8VI for ; Wed, 22 Jun 2022 15:57:55 +0200 (CEST) Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 22 Jun 2022 15:57:55 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.9; Wed, 22 Jun 2022 15:57:54 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-aseb. Date: Wed, 22 Jun 2022 15:57:41 +0200 Message-ID: <20220622135741.16618-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-AS-Result: No-10-0.211700-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzFIcsAc8jehkqa6TyhyXvPbqL 7Fma/TB8hHr+pkQiTeJ+XXzWmAMTULmsVDuK2FjyQJOFc+qyqK83dpdHr49yZ64sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJShNCXvA0fw+jaPj0W1qn0TKayT/BQTiGqr9r fzj4GbEcReVTV/zMZmjvBzjRJE72EDr7D5ZwrlJM5L6Azz9MyNiSpMo2OO7ky6FyX3DDsVUxspd MdNUyuAv8O7hvDpIuy24H4xRId62tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfQ5+gyyDasGNDDKa 3G4nrLQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.211700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-SNTS-SMTP: D2ADA119C79201734F3C88B261FBE2BDF8D94596C1E2F626AA88167CFCB0A1E52002: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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-aseb): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..f961d201d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,32 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-aseb + (package + (name "r-aseb") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASEB" version)) + (sha256 + (base32 + "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + (properties `((upstream-name . "ASEB"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/ASEB") + (synopsis "Predict acetylated lysine sites") + (description + "@code{ASEB} is an R package to predict lysine sites that can be acetylated +by a specific @dfn{KAT}-family (K-acetyl-transferases). Lysine acetylation is +a well-studied posttranslational modification on kinds of proteins. About four +thousand lysine acetylation sites and over 20 lysine KATs have been identified. +However, which KAT is responsible for a given protein or lysine site acetylation +is mostly unknown. In this package, we use a @dfn{GSEA}-like (Gene Set Enrichment +Analysis) method to make predictions. GSEA method was developed and successfully +used to detect coordinated expression changes and find the putative functions +of the long non-coding RNAs.") + (license license:gpl3+))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 ------------=_1667249222-6739-1--