[adegenet-commits] r1118 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 25 19:08:20 CEST 2013
Author: jombart
Date: 2013-04-25 19:08:19 +0200 (Thu, 25 Apr 2013)
New Revision: 1118
Modified:
www/acceuil.html
Log:
modified the frontpage - adding contributors info
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2013-04-25 16:32:37 UTC (rev 1117)
+++ www/acceuil.html 2013-04-25 17:08:19 UTC (rev 1118)
@@ -1,7 +1,7 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
- <meta content="text/html; charset=ISO-8859-1"
+ <meta content="text/html; charset=windows-1252"
http-equiv="content-type">
<title>adegenet on the web</title>
<script type="text/javascript">
@@ -18,151 +18,160 @@
</script>
</head>
<body>
- <div style="margin-left: 40px; text-align: center;">
- <img style="width: 600px; height: 90px;" alt="title"
+ <div style="margin-left: 40px; text-align: center;"> <img
+ style="width: 600px; height: 90px;" alt="title"
src="images/title.png"><br>
<br>
<br>
<br>
- <div style="text-align: left;">
- <span style="font-weight: bold;">adegenet</span> is an <span
- style="text-decoration: underline;"><a
+ <div style="text-align: left;"> <span style="font-weight: bold;">adegenet</span>
+ is an <span style="text-decoration: underline;"><a
href="http://www.r-project.org/" target="_top"><img alt=""
src="images/R.png" style="border: 0px solid ; width: 30px;
- height: 23px;"></a></span> package
- dedicated to the exploratory analysis of genetic data. It
- implements a set of
+ height: 23px;"></a></span> package dedicated to the
+ exploratory analysis of genetic data. It implements a set of
tools ranging from multivariate methods to spatial genetics and
- genome-wise SNP
- data analysis. <br>
+ genome-wise SNP data analysis. <br>
<br>
It is developed on <a
href="https://r-forge.r-project.org/projects/adegenet/"
target="_top">R-Forge</a> by <a
href="http://sites.google.com/site/thibautjombart/">Thibaut
- Jombart</a>, Ismail
- Ahmed, Anne Cori, Tobias Erik Reiners, and Péter
- Sólymos, and officially released on <a
- href="http://cran.r-project.org">CRAN</a> periodically. <br>
+ Jombart</a>, Ismail Ahmed, <a
+ href="https://www1.imperial.ac.uk/medicine/people/f.calboli/">Federico
+
+ Calboli</a>, <a
+ href="http://www1.imperial.ac.uk/medicine/people/a.cori/">Anne
+ Cori</a>, Tobias Erik Reiners, and <a
+ href="https://sites.google.com/site/psolymos/">Péter Sólymos</a>,
+ and officially released on <a href="http://cran.r-project.org">CRAN</a>
+ periodically. <br>
<br>
adegenet is described in the following application notes:<br>
<span style="font-style: italic;"></span>Jombart T. (<span
style="font-style: italic;"></span>2008)<span
- style="font-weight: bold;"></span>adegenet: a R package for
- the multivariate
- analysis of genetic markers. <span style="font-style: italic;">Bioinformatics</span>
- <span style="font-weight: bold;">24</span>: 1403-1405. doi:
+ style="font-weight: bold;"></span> adegenet: a R package for
+ the multivariate analysis of genetic markers. <span
+ style="font-style: italic;">Bioinformatics</span> <span
+ style="font-weight: bold;">24</span>: 1403-1405. doi:
10.1093/bioinformatics/btn129 [<a
href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a>
to a free pdf]<br>
<br>
Jombart T. and Ahmed I. (2011) <span style="font-style:
- italic;">adegenet
- 1.3-1</span>: new tools for the analysis of genome-wide SNP
- data. <span style="font-style: italic;">Bioinformatics</span>.
- doi:
- 10.1093/bioinformatics/btr521 [<a
+ italic;">adegenet 1.3-1</span>: new tools for the analysis of
+ genome-wide SNP data. <span style="font-style: italic;">Bioinformatics</span>.
+ doi: 10.1093/bioinformatics/btr521 [<a
href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
to
+
+
the bublisher's website</a>]<br>
<br>
<br>
- <div style="text-align: center;">
- <img style="width: 600px; height: 451px;" alt=""
- src="images/acceuil.png" height="788" width="1044"><br>
+ <div style="text-align: center;"> <img style="width: 600px;
+ height: 451px;" alt="" src="images/acceuil.png" height="788"
+ width="1044"><br>
<br>
</div>
<div style="text-align: left;">
- <div style="text-align: center;">
- <small>sPCA, DAPC, typological coherence of markers,
- Monmonier algorithm,
- ...<br>
+ <div style="text-align: center;"> <small>sPCA, DAPC,
+ typological coherence of markers, Monmonier
+ algorithm, ...<br>
<br>
</small></div>
<small><br>
</small><span style="text-decoration: underline;">Main
- features of adegenet
- are:</span><br>
+ features of adegenet are:</span><br>
- data representation (<span style="font-weight: bold;">classes</span>)
suitable for multivariate analysis<br>
</div>
- data <span style="font-weight: bold;">import</span> from
- GENETIX, STRUCTURE,
- Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
+ GENETIX, STRUCTURE, Genepop, Fstat, Easypop, or any dataframe of
+ genotypes<br>
- data import from <span style="font-weight: bold;">aligned DNA
sequences</span> to <span style="font-weight: bold;">SNPs</span><br>
- data import from <span style="font-weight: bold;">aligned
- protein
- sequences</span> to polymorphic sites<span style="font-weight:
- bold;"></span>
- <br>
+ protein sequences</span> to polymorphic sites<span
+ style="font-weight: bold;"></span> <br>
- data <span style="font-weight: bold;">export</span> to the R
- packages
- genetics, hierfstat, LDheatmap<br>
+ packages genetics, hierfstat, LDheatmap<br>
- handling of <span style="font-weight: bold;">different levels
of ploidy<br>
</span>- handling of <span style="font-weight: bold;">codominant
+
+
</span>markers<span style="font-weight: bold;"></span>and<span
style="font-weight: bold;">presence/absence</span> data<span
style="font-weight: bold;"><br>
</span>- basic and advanced <span style="font-weight: bold;">data
+
+
manipulation</span><br>
- - basic <span style="font-weight: bold;">data information
- </span>(heterozygosity, numbers of alleles, sample sizes, ...)<br>
+ - basic <span style="font-weight: bold;">data information </span>(heterozygosity,
+
+ numbers of alleles, sample sizes, ...)<br>
- <span style="font-weight: bold;">HWE</span> and <span
style="font-weight: bold;">G-statistic</span> <span
style="font-weight: bold;">tests</span>, F statistics
- implemented for adegenet
- objects<br>
+ implemented for adegenet objects<br>
- computation of <span style="font-weight: bold;">genetic</span>
<span style="font-weight: bold;">distances<br>
</span>- computation of <span style="font-weight: bold;">pairwise
- Fst
- </span><br>
+
+
+ Fst </span><br>
- simulation of <span style="font-weight: bold;">hybridization<br>
</span><span style="font-weight: bold;"></span>- methods for <span
style="font-weight: bold;">spatial genetics: sPCA, </span><span
style="font-weight: bold;">tests for global and local
structuring, </span><span style="font-weight: bold;">Monmonier
+
+
algorithm<br>
</span>- the <span style="font-style: italic; font-weight:
bold;">seqTrack</span><span style="font-weight: bold;">algorithm
- </span>for reconstructing genealogies of
- haplotypes<span style="font-weight: bold;"><br>
+
+
+ </span>for reconstructing genealogies of haplotypes<span
+ style="font-weight: bold;"><br>
</span>- simulation of <span style="font-weight: bold;">genealogies
- of
- haplotypes</span><br>
+
+
+ of haplotypes</span><br>
- Discriminant Analysis of Principal Components (<span
style="font-weight: bold;">DAPC</span>)<span
style="font-weight: bold;"></span><br>
- efficient genome-wise SNP data handling and analysis <br>
- <b>extraction of SNPs</b> from genomic alignments <br>
- <span style="font-weight: bold;">graph-based clustering</span>
- of genomic
- data<br>
+ of genomic data<br>
- identification of mutations between pairs of sequences <img
style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
<span style="font-weight: bold;"><br>
<span style="text-decoration: underline; font-weight: bold;">Maintainer</span></span><span
style="text-decoration: underline; font-weight: bold;">:</span>
- Thibaut Jombart
- (<a target="_new"
+ Thibaut Jombart (<a target="_new"
href="http://sites.google.com/site/thibautjombart/">website</a>)<br>
<span style="text-decoration: underline;">Developers:</span>
- Thibaut Jombart
- (<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>),
- Ismaïl
- Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
-Anne
- Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
+ Thibaut Jombart (<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>),
+
+
+ Ismaïl Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
+Federico
+ Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
+ Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
Tobias
+
+
Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
- Péter Sólymos<br>
+
+
+ Péter Sólymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
<span style="text-decoration: underline;">Contributors
(datasets/ideas):</span> Christophe Fraser, Katayoun
- Moazami-Goudarzi, Denis Laloë, Francois Balloux, Dominique
- Pontier, Daniel
- Maillard<span style="font-weight: bold;"><br>
+ Moazami-Goudarzi, Denis Laloë, Francois Balloux, Dominique
+ Pontier, Daniel Maillard<span style="font-weight: bold;"><br>
<br>
<br style="font-weight: bold;">
Suggestions, comments and contributions are most welcome!</span><br>
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