[adegenet-commits] r928 - in www: . files images images/gimp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 27 13:37:21 CEST 2011
Author: jombart
Date: 2011-06-27 13:37:21 +0200 (Mon, 27 Jun 2011)
New Revision: 928
Added:
www/images/dapc1.png
www/images/dapc2.png
www/images/dapc3.png
www/images/gimp/
www/images/gimp/acceuil-old.xcf
www/images/gimp/acceuil.xcf
www/images/rupica.png
www/images/spca1.png
www/images/title.png
www/images/title.xcf
www/images/titre-old.png
www/images/titre-old.xcf
Removed:
www/images/titre.png
www/images/titre.xcf
Modified:
www/acceuil.html
www/files/adegenet_1.3-0.tar.gz
www/images/acceuil.png
www/literature.html
www/news.html
www/screenshots.html
Log:
Updated website for new release.
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2011-06-24 07:54:07 UTC (rev 927)
+++ www/acceuil.html 2011-06-27 11:37:21 UTC (rev 928)
@@ -20,32 +20,27 @@
</head>
<body>
<div style="margin-left: 40px; text-align: center;"><img
- style="width: 524px; height: 103px;" alt="" src="images/titre.png"><br>
+ 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 a <span style="text-decoration: underline;"><a
+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 multivariate analysis of genetic
-markers. This package is related to <a
- href="http://pbil.univ-lyon1.fr/ADE-4/home.php?lang=eng" target="_top">ade4</a>,
-a
-R
-package
-for
-multivariate
-analysis,
-graphics,
-phylogeny
-and spatial
-analysis. It is kindly hosted by <a
- href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
+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>
<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> and Ismail Ahmed, and officially released on <a
+ href="http://cran.r-project.org">CRAN</a> periodically.
+<br>
+<br>
adegenet is described in the following application note:<br>
-<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
@@ -62,9 +57,8 @@
<br>
</div>
<div style="text-align: left;">
-<div style="text-align: center;"><small>sPCA, typological
-coherence of markers, Monmonier algorithm,
-colorplot of genotypes, analyses using ade4, ...<br>
+<div style="text-align: center;"><small>sPCA, DAPC, typological
+coherence of markers, Monmonier algorithm, ...<br>
<br>
</small></div>
<small><br>
@@ -79,7 +73,7 @@
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>
-<img style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<br>
- data <span style="font-weight: bold;">export</span> to the R
packages genetics, hierfstat, LDheatmap<br>
- handling of <span style="font-weight: bold;">different levels of
@@ -103,8 +97,7 @@
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><img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+</span>- computation of <span style="font-weight: bold;">pairwise 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
@@ -117,30 +110,37 @@
algorithm </span>for reconstructing genealogies of haplotypes<span
style="font-weight: bold;"><br>
</span>- simulation of <span style="font-weight: bold;">genealogies of
-haplotypes</span><img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+haplotypes</span><br>
- Discriminant Analysis of Principal Components (<span
style="font-weight: bold;">DAPC</span>)<span style="font-weight: bold;">
-</span><img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+</span><br>
+- efficient genome-wise SNP data handling and analysis <img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+- extraction of SNP data from genomic alignments <img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
<span style="font-weight: bold;"><br>
-<span style="text-decoration: underline;">Maintainer</span></span><span
- style="text-decoration: underline;">:</span> Thibaut
+<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" 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>),
+Ismaïl
+Ahmed
+(<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>)<br>
+<span style="text-decoration: underline;">Contributors
+(functions/datasets):</span>
Péter
-Sólymos<br>
-<span style="text-decoration: underline;">Contributors:</span>
-Francois Balloux, Katayoun Moazami-Goudarzi & Denis Laloë,
-Dominique Pontier, Daniel Maillard, Francois Balloux<br>
-<span style="font-weight: bold;"><br>
-</span>Suggestions, remarks and contributions are greatly encouraged!<br>
+Sólymos, Francois Balloux, Katayoun Moazami-Goudarzi & Denis
+Laloë,
+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>
<br>
<br>
+<br>
<span style="font-weight: bold;"></span></div>
</div>
</body>
Modified: www/files/adegenet_1.3-0.tar.gz
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+ *
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+ *
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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===================================================================
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___________________________________________________________________
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+ application/octet-stream
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(Binary files differ)
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Added: svn:mime-type
+ application/octet-stream
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===================================================================
(Binary files differ)
Modified: www/literature.html
===================================================================
--- www/literature.html 2011-06-24 07:54:07 UTC (rev 927)
+++ www/literature.html 2011-06-27 11:37:21 UTC (rev 928)
@@ -457,15 +457,20 @@
style="font-style: italic;">in press</span>) Human impact on genetic
diversity of <span style="font-style: italic;">Toxoplasma gondii</span>:
Example
-of the anthropized environment from French Guiana. <br>
+of
+the anthropized environment from French Guiana. <br>
Infection, Genetics and Evolution.<br>
</p>
<p class="intro">[39] MONTANO, V., FERRI, G., MARCARI, V., BATINI, C.,
ANYAELE, O., DESTRO-BISOL, G. and COMAS, D. (2011), The Bantu expansion
revisited: a new analysis of Y chromosome variation in Central Western
Africa. Molecular Ecology, 20: no.
-doi: 10.1111/j.1365-294X.2011.05130.x
+doi: 10.1111/j.1365-294X.2011.05130.x<br>
</p>
+<p class="intro">[40] GAUTIER, M. and NAVES, M. (2011), Footprints of
+selection in the ancestral admixture of a New World Creole cattle
+breed. Molecular Ecology, 20: no.
+doi: 10.1111/j.1365-294X.2011.05163.x</p>
<span class="citation_doi"></span><span style="display: block;"
id="records_chunks"></span><span class="citation_author"></span><span
class="citation_doi"></span>
Modified: www/news.html
===================================================================
--- www/news.html 2011-06-24 07:54:07 UTC (rev 927)
+++ www/news.html 2011-06-27 11:37:21 UTC (rev 928)
@@ -28,17 +28,14 @@
<br>
<span style="font-weight: bold;"><big><br>
</big></span><span style="font-weight: bold;"><big>Coming soon</big></span><br>
-Next release (1.3-0) is currently being released on CRAN. It will
-include a lot of new material,
-tutorials in the form of vignettes, new DAPC functionalities, and the
-most efficient handling of genome-wide SNPs data existing to date.<br>
+Next release (1.3-1) is under development.<br>
<br>
<br>
<span style="font-weight: bold;"><big>Today</big> </span><span
style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
<span style="font-weight: bold;"></span>Current
stable version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.2-8 </span>for R.2.13.0.<br>
+1.3-0 </span>for R.2.13.0.<br>
You can install the devel version from <a
href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
See the current <a
@@ -46,15 +43,36 @@
for a list of
all modifications.<br>
<br>
+<span style="font-weight: bold;">27/06/2011 </span><span
+ style="font-weight: bold;"></span><img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-0</span>)
+has
+been
+released
+for
+R-2.13.0!</big><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">
+This new major release implements new classes and methods for the
+handling and analysis of genome-wide SNP data, along with several
+improvements to previous tools (especially new graphics for DAPC) </span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">and
+a few bug fixes. It also include 4 new tutorial distributed as
+vignettes. See the </span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"></span></span><a
+ href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+file for details of the release.</span></span> Given this is a major
+release, version number switched directly from 1.2-8 to 1.3-0.<br>
<br>
-<span style="font-weight: bold;">02/06/2011 </span><img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<br>
+<span style="font-weight: bold;">02/06/2011</span><br>
A new tutorial dedicated to DAPC has been uploaded on the website (see
section "documents").<br>
<br>
<br>
-<span style="font-weight: bold;">14/12/2010 </span><img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<span style="font-weight: bold;">14/12/2010 </span><br>
<span style="font-weight: bold;">The DAPC paper has been nicely
reviewed by Laurent Excoffier on Faculty of 1000</span> [<a
href="reviewDAPC.html">see evaluation</a>].<br>
@@ -320,7 +338,8 @@
alleles
and
loci
-in an
+in
+an
analysis. A new georeferenced genetic dataset is also available
(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
And...
Modified: www/screenshots.html
===================================================================
--- www/screenshots.html 2011-06-24 07:54:07 UTC (rev 927)
+++ www/screenshots.html 2011-06-27 11:37:21 UTC (rev 928)
@@ -1,10 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="content-type">
<title>documentation</title>
-<script type="text/javascript">
+ <script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -16,38 +16,46 @@
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
-</script>
+ </script>
</head>
<body>
<br>
<br>
<br>
<div style="margin-left: 40px;">Here are a few pictures of adegenet
-version 1.1-0 working on a linux system. Users are encouraged
+version 1.3-0 working on a linux system. Users are encouraged
to submit their own artwork.<br>
<br>
-Adegenet loading:<br>
+DAPC of simulated data with superimposed minimum spanning tree:<br>
+<img style="width: 500px; height: 500px;" alt="" src="images/dapc1.png"><br>
<br>
-<img alt="" src="images/sshotstart.png"
- style="width: 500px; height: 349px;"><br>
-<br>
</div>
<br>
- The printing of a genind object:<br>
+ <br>
+ DAPC of H3N2 dataset:<br>
+ <img
+ style="width: 500px; height: 500px;" alt="" src="images/dapc2.png"><br>
<br>
- <img
- style="width: 600px; height: 439px;" alt=""
- src="images/sshotgenind.png"><br>
<br>
+ DAPC plot of group membership
+(compoplot), microbov dataset:<br>
+ <img
+ style="width: 500px; height: 500px;" alt="" src="images/dapc3.png"><br>
+ <br>
<br>
- The printing of a genpop object:<br>
+ Interpolation and mapping of sPCA
+scores (simulated data):<br>
+ <img
+ style="width: 500px; height: 500px;" alt="" src="images/spca1.png"><br>
<br>
- <img
- style="width: 600px; height: 439px;" alt=""
- src="images/sshotgenpop.png"><br>
+ sPCA colorplot of the rupica
+dataset:<br>
+ <img
+ style="width: 500px; height: 500px;" alt="" src="images/rupica.png"><br>
<br>
+ <br>
Multiple co-inertia analysis in
-the example of microbov dataset (click to enlarge):<br>
+the example of microbov dataset:<br>
<br>
<a href="sshotmicrobov.html"><img
alt="" src="images/sshotmicrobov-prev.png"
@@ -60,6 +68,8 @@
alt="" src="images/sshotmonmonier-prev.png"
style="border: 0px solid ; width: 512px; height: 279px;"></a><br>
<br>
+<br>
+ <br>
<br>
</body>
</html>
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