From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add eigensoft. Date: Wed, 13 Jul 2016 08:38:15 +0200 Message-ID: <87wpkq11rc.fsf@mdc-berlin.de> References: <20160712132919.20938-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56062) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bNDoW-0006Xq-3l for guix-devel@gnu.org; Wed, 13 Jul 2016 02:38:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bNDoQ-0001MA-5e for guix-devel@gnu.org; Wed, 13 Jul 2016 02:38:31 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:48979) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bNDoP-0001M4-R8 for guix-devel@gnu.org; Wed, 13 Jul 2016 02:38:26 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 138DA380DDA for ; Wed, 13 Jul 2016 08:38:24 +0200 (CEST) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id UrpGbtAQccyS for ; Wed, 13 Jul 2016 08:38:18 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 13 Jul 2016 08:38:18 +0200 (CEST) In-Reply-To: <20160712132919.20938-1-ricardo.wurmus@mdc-berlin.de> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org Ricardo Wurmus writes: > * gnu/packages/bioinformatics.scm (eigensoft): New variable. [=E2=80=A6] > + (description "This package provides tools for population genetic= s and > +stratification correction. The EIGENSTRAT method uses principal compo= nents > +analysis to explicitly model ancestry differences between cases and co= ntrols > +along continuous axes of variation; the resulting correction is specif= ic to a > +candidate marker=E2=80=99s variation in frequency across ancestral pop= ulations, > +minimizing spurious associations while maximizing power to detect true > +associations. The EIGENSOFT package has a built-in plotting script an= d > +supports multiple file formats and quantitative phenotypes.") Here=E2=80=99s an alternative description, which is a little more general= and doesn=E2=80=99t emphasise EIGENSTRAT so much: The EIGENSOFT package provides tools for population genetics and stratification correction. EIGENSOFT implements methods commonly used in population genetics analyses such as PCA, computation of Tracy-Widom statistics, and finding relateds in structured populations. It comes with a built-in plotting script and supports multiple file formats and quantitative phenotypes. WDYT? ~~ Ricardo