[adegenet-commits] r1158 - in www: . images images/gimp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 14 16:01:47 CET 2014
Author: jombart
Date: 2014-03-14 16:01:47 +0100 (Fri, 14 Mar 2014)
New Revision: 1158
Added:
www/images/sshotdapcserver1.png
www/images/sshotdapcserver2.png
www/images/sshotdapcserver3.png
Modified:
www/acceuil.html
www/images/acceuil.png
www/images/gimp/acceuil.xcf
www/news.html
www/screenshots.html
Log:
updated website
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2013-12-03 04:28:29 UTC (rev 1157)
+++ www/acceuil.html 2014-03-14 15:01:47 UTC (rev 1158)
@@ -37,7 +37,9 @@
by <a href="http://sites.google.com/site/thibautjombart/">Thibaut
- Jombart</a>, Ismail Ahmed, Caitlin Collins, <a
+
+
+ Jombart</a>, Caitlin Collins, Ismail Ahmed, <a
href="http://www.federicocalboli.com/">Federico Calboli</a>, <a
href="http://www1.imperial.ac.uk/medicine/people/a.cori/">Anne
Cori</a>, Tobias Erik Reiners, and <a
@@ -45,21 +47,21 @@
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:
- 10.1093/bioinformatics/btn129 [<a
+ adegenet is described in the following publications:<br>
+ <ul>
+ <li> Jombart T. (2008) 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
+ to a free pdf]<br>
+ <br>
+ </li>
+ <li>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
href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
to
@@ -67,9 +69,12 @@
- the bublisher's website</a>]<br>
+
+
+ the bublisher's website</a>]<br>
+ </li>
+ </ul>
<br>
- <br>
<div style="text-align: center;"> <img style="width: 600px;
height: 451px;" alt="" src="images/acceuil.png" height="788"
width="1044"><br>
@@ -84,92 +89,98 @@
<small><br>
</small><span style="text-decoration: underline;">Main
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>
- - 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>
- - 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 ploidy<br>
- </span>- handling of <span style="font-weight: bold;">codominant
+ <ul>
+ <li>data representation (<span style="font-weight: bold;">classes</span>)
+ suitable for multivariate analysis</li>
+ <li>data <span style="font-weight: bold;">import</span>
+ from GENETIX, STRUCTURE, Genepop, Fstat, Easypop, or any
+ dataframe of genotypes</li>
+ <li>data import from <span style="font-weight: bold;">aligned
+ DNA sequences</span> to <span style="font-weight:
+ bold;">SNPs</span></li>
+ <li> data import from <span style="font-weight: bold;">aligned
+ protein sequences</span> to polymorphic sites </li>
+ <li> data <span style="font-weight: bold;">export</span> to
+ the R packages genetics, hierfstat, LDheatmap</li>
+ <li> handling of <span style="font-weight: bold;">different
+ levels of ploidy</span></li>
+ <li>handling of <span style="font-weight: bold;">codominant
+ </span>markersand<span style="font-weight: bold;">presence/absence</span>
+ data</li>
+ <li>basic and advanced <span style="font-weight: bold;">data
- </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,
+ manipulation</span></li>
+ <li> basic <span style="font-weight: bold;">data
+ information </span>(heterozygosity, numbers of alleles,
+ sample sizes, ...)</li>
+ <li> <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</li>
+ <li> computation of <span style="font-weight: bold;">genetic</span>
+ <span style="font-weight: bold;">distances</span></li>
+ <li>computation of <span style="font-weight: bold;">pairwise
- 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>
- - 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></li>
+ <li> simulation of <span style="font-weight: bold;">hybridization</span></li>
+ <li>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</span></li>
+ <li>the <span style="font-style: italic; font-weight:
+ bold;">seqTrack</span><span style="font-weight: bold;">algorithm
- 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</li>
+ <li>simulation of <span style="font-weight: bold;">genealogies
- </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>
- - 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>
- - identification of mutations between pairs of sequences <img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+ of haplotypes</span></li>
+ <li> Discriminant Analysis of Principal Components (<span
+ style="font-weight: bold;">DAPC</span>)</li>
+ <li> efficient genome-wise SNP data handling and analysis </li>
+ <li> <b>extraction of SNPs</b> from genomic alignments </li>
+ <li> <span style="font-weight: bold;">graph-based
+ clustering</span> of genomic data</li>
+ <li> identification of mutations between pairs of sequences
+ </li>
+ <li><b>visualization of SNPs density</b> and test for the
+ randomness of their distribution<img style="width: 80px;
+ height: 37px;" alt="" src="images/new.png" height="37"
+ width="80"></li>
+ <li><b>web interface for DAPC</b>, including feature
+ selection and cross validation <img style="width: 80px;
+ height: 37px;" alt="" src="images/new.png" height="37"
+ width="80"><br>
+ </li>
+ </ul>
+ </div>
<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>
@@ -177,18 +188,26 @@
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>),
+Caitlin
+ Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
+
+
+
+
Ismaïl Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
-Caitlin
- Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins17 at gmail.com</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
@@ -196,12 +215,16 @@
+
+
Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
+
+
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
Modified: www/images/acceuil.png
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+ application/octet-stream
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Added: svn:mime-type
+ application/octet-stream
Modified: www/news.html
===================================================================
--- www/news.html 2013-12-03 04:28:29 UTC (rev 1157)
+++ www/news.html 2014-03-14 15:01:47 UTC (rev 1158)
@@ -28,30 +28,63 @@
0, 0);"></span><br>
<br>
<span style="font-weight: bold;">What's next<big></big></span>?<br>
- Next release (1.4-0) is under development.<br>
+ Next release (1.4-1) 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 1.3-9 </span>for
- R.3.0.1.<br>
- You can install the devel version from <a
- href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
+ <span style="color: rgb(255, 0, 0);">adegenet is 1.4-0 </span>for
+ R.3.0.3.<br>
See the current <a
href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a>
for a list of all modifications.<br>
<br>
<br>
- 28/06/2013 <img style=" width: 80px; height: 37px;" alt=""
- src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+ 14/03/2014 <img style=" width: 80px; height: 37px;" alt=""
+ src="images/new.png" height="37" width="80"><br>
+ <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.4-0</span>)
+ has been released for R-3.0.3!</big> <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
+ include a web interface for DAPC </span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);"><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);"><span
+ style="color: rgb(255, 0, 0);"><span style="color:
+ rgb(0, 0, 0);"><span style="font-family: monospace;
+ color: rgb(255, 0, 0);">adegenetServer</span></span><span
+ style="font-family: monospace;"></span><span
+ style="color: rgb(0, 0, 0);"></span></span>)</span></span>,
+ improvements of the DAPC cross-validation procedure for small
+ sample sizes, visualization and test of the SNP density on
+ alignments (</span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><span style="color: rgb(255, 0,
+ 0);"><span style="color: rgb(0, 0, 0);"><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">snpposi.plot,snpposi.test</span></span></span>),
+
+ and DAPC-based feature selection (</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);"><span style="color: rgb(255, 0, 0);"><span style="color:
+ rgb(0, 0, 0);"><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><span style="font-family:
+ monospace; color: rgb(255, 0, 0);">snpzip</span></span></span></span></span>).
+
+ </span><span style="color: rgb(0, 0, 0);">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 more details.</span></span><br>
+ <br>
+ 28/06/2013 <br>
Caitlin Collins has joined the development team, and will be
- implementing DAPC-basec feature-selection procedures.<br>
+ implementing DAPC-based feature-selection procedures.<br>
<br>
<br>
- 18/06/2013 <img style=" width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+ 18/06/2013 <br>
The development of adegenet has now moved on Sourceforge. The
adegenet website will remain at its current place. More on:<br>
<a href="https://sourceforge.net/projects/adegenet/">https://sourceforge.net/projects/adegenet/</a><br>
@@ -125,6 +158,8 @@
+
+
with a possibility of visualization using graphs (</span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
0);"><span style="color: rgb(255, 0, 0); font-family:
@@ -216,6 +251,8 @@
+
+
</span>package seems to be gone for good from CRAN, but the
documentation shows how to use <span style="color: rgb(255, 0,
0); font-family: monospace;">Fst</span> from the <span
@@ -455,6 +492,8 @@
+
+
time, the tutorial has been updated at the same time as the
package release!<br>
<br>
@@ -596,6 +635,8 @@
+
+
The function <span style="font-family: monospace; color: rgb(255,
0, 0);">chooseCN</span> has a new option to return a list of
spatial weights defined as the inverse of spatial distances, at a
@@ -637,6 +678,8 @@
+
+
Principal Component Analysis (Jombart et al, submitted to
Heredity), two multivariate spatial tests, and new functionalities
for Monmonier's algorithm.<br>
@@ -656,6 +699,8 @@
+
+
manipulation:</span> new function to separate data by
population. Accessors to genind and genpop object like with
matrices using 'foo[ chosenGenotypes, chosenAlleles]'.<br>
@@ -705,6 +750,8 @@
+
+
using <span style="font-family: monospace; color: rgb(255, 0,
0);">sim2pop</span><span style="color: rgb(255, 0, 0);"> </span>data.<br>
<span style="font-weight: bold;"><br>
Modified: www/screenshots.html
===================================================================
--- www/screenshots.html 2013-12-03 04:28:29 UTC (rev 1157)
+++ www/screenshots.html 2014-03-14 15:01:47 UTC (rev 1158)
@@ -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">
+ <head>
+ <meta content="text/html; charset=windows-1252"
+ http-equiv="content-type">
+ <title>documentation</title>
+ <script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -17,59 +17,77 @@
})();
</script>
-</head>
-<body>
-<br>
-<br>
-<br>
-<div style="margin-left: 40px;">Here are a few pictures of adegenet
-version 1.3-0 working on a linux system. Users are encouraged
-to submit their own artwork.<br>
-<br>
-DAPC of simulated data with superimposed minimum spanning tree:<br>
-<img style="width: 500px; height: 500px;" alt="" src="images/dapc1.png"><br>
-<br>
-</div>
-<br>
- <br>
- DAPC of H3N2 dataset:<br>
- <img
- style="width: 500px; height: 500px;" alt="" src="images/dapc2.png"><br>
-<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>
- Interpolation and mapping of sPCA
-scores (simulated data):<br>
- <img
- style="width: 500px; height: 500px;" alt="" src="images/spca1.png"><br>
-<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:<br>
- <br>
- <a href="sshotmicrobov.html"><img
- alt="" src="images/sshotmicrobov-prev.png"
- style="border: 0px solid ; width: 512px; height: 378px;"></a><br>
-<br>
-<br>
- Monmonier algorithm example:<br>
-<br>
- <a href="sshotmonmonier.html"><img
- alt="" src="images/sshotmonmonier-prev.png"
- style="border: 0px solid ; width: 512px; height: 279px;"></a><br>
- <br>
-<br>
- <br>
- <br>
-</body>
+ </head>
+ <body>
+ <br>
+ <br>
+ <br>
+ <div style="margin-left: 40px;">Here are a few pictures of adegenet
+ version 1.4-0 working on a linux system. Users are encouraged
+ to submit their own artwork.<br>
+ <br>
+ DAPC server - one dimensional scatterplot:<br>
+ <img alt="" src="images/sshotdapcserver1.png" height="572"
+ width="800"><br>
+ <br>
+ <br>
+ DAPC server - two-dimensional scatterplot:<br>
+ <img alt="" src="images/sshotdapcserver2.png" height="572"
+ width="800"><br>
+ <br>
+ <br>
+ DAPC server - cross-validation:<br>
+ <img alt="" src="images/sshotdapcserver3.png" height="572"
+ width="800"><br>
+ <br>
+ <br>
+ DAPC of simulated data with superimposed minimum spanning tree:<br>
+ <img style="width: 500px; height: 500px;" alt=""
+ src="images/dapc1.png"><br>
+ <br>
+ </div>
+ <br>
+ <br>
+ DAPC of H3N2 dataset:<br>
+ <img style="width: 500px;
+ height: 500px;" alt="" src="images/dapc2.png"><br>
+ <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>
+ Interpolation and mapping of
+ sPCA
+ scores (simulated data):<br>
+ <img style="width: 500px;
+ height: 500px;" alt="" src="images/spca1.png"><br>
+ <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:<br>
+ <br>
+ <a href="sshotmicrobov.html"><img
+ alt="" src="images/sshotmicrobov-prev.png" style="border: 0px
+ solid ; width: 512px; height: 378px;"></a><br>
+ <br>
+ <br>
+ Monmonier algorithm example:<br>
+ <br>
+ <a href="sshotmonmonier.html"><img
+ 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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