[adegenet-commits] r1080 - in www: . files
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 3 19:43:06 CET 2013
Author: jombart
Date: 2013-03-03 19:43:05 +0100 (Sun, 03 Mar 2013)
New Revision: 1080
Added:
www/files/seqTrack-practical.1.2.pdf
Modified:
www/documentation.html
Log:
Adding practical for RAPID-NGS in M?\195?\188nster
Modified: www/documentation.html
===================================================================
--- www/documentation.html 2013-03-03 17:41:58 UTC (rev 1079)
+++ www/documentation.html 2013-03-03 18:43:05 UTC (rev 1080)
@@ -1,10 +1,10 @@
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<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=ISO-8859-1"
+ http-equiv="content-type">
+ <title>documentation</title>
+ <script type="text/javascript">
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@@ -16,119 +16,148 @@
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})();
</script>
-</head>
-<body>
-<br>
-<br>
-<br>
-<div style="margin-left: 40px;">As a <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, each component of adegenet is documented in help pages. As a
-starting point, one can type <span
- style="font-family: monospace; font-weight: bold;">?adegenet</span> in
-R to get an overview of package. Other sources of information
-distributed with the package include a manual and vignettes. This
-website also provides other resources such as lectures and practicals.<br>
-<br>
-<span style="font-weight: bold;">To search quickly</span> through these
-resources, use the <a target="_top" href="search.html">search engine</a>.
-<img style="width: 80px; height: 37px;" alt="new" src="images/new.png"><br>
-<br>
-<br>
-<br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);">Manuals</span><br>
-- the adegenet <span style="font-weight: bold;">manual</span> (<a
- href="files/adegenet-manual.pdf">pdf</a>), which compiles all the
-manpages of the package.<br>
-<br>
-<br>
-<span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
-vignettes </span><br>
-- <a href="files/adegenet-basics.pdf"><span style="font-style: italic;">adegenet-basics</span></a>:
-
-introduction
-to the package; accessible from R by typing <span
- style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-basics")</span>.<br>
-</div>
- - <a
- href="files/adegenet-spca.pdf"><span style="font-style: italic;">adegenet-spca</span></a>:
-
-spatial
-multivariate analysis using adegenet; includes an introduction
-to spatial PCA (sPCA); accessible from R by typing <span
- style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-spca")</span>.<br>
-<div style="margin-left: 40px;">- <a href="files/adegenet-dapc.pdf"><span
- style="font-style: italic;">adegenet-dapc</span></a>: analysis of the
-genetic structuring of populations; includes an introduction to
-Discriminant Analysis of Principal Components (DAPC); accessible from R
-by typing <span style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-dapc")</span>.<br>
-- <a href="files/adegenet-genomics.pdf"><span
- style="font-style: italic;">adegenet-genomics</span></a>: introduction
-to the handling of genome-wide SNP data using adegenet; accessible from
-R by typing <span
- style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-genomics")</span>.<br>
-<br>
- <br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);">Lectures and
-practicals</span><br>
-- globaldiv summer school 2009, Piacenza, Italie: <a
- href="files/globaldiv-TJ.1.3.pdf">talk</a> - <a
- href="files/globaldiv-PC.1.3.pdf">practical course</a><br>
-<br>
-- Master 2 "Ecology, Evolution, Biometry", Lyon, France: <a
- href="files/talk-E2B.1.0.pdf">talk</a> - <a href="files/TD-E2B.pdf">practical
-course</a><br>
-<br>
-- One-week course on Genetic Data Analysis, Bogota, Colombia: <br>
- > <a href="files/day1.1.2.pdf">lecture 1</a>:
-methodological overview<br>
- > <a href="files/day2.1.3.pdf">lecture 2</a>:
-finding clusters, using cluster information<br>
- > <a href="files/day3.1.2.pdf">lecture 3</a>:
-spatial genetics<br>
- > <a href="files/practical-day1.1.2.pdf">practical
-1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version with all
-commands</a>]<br>
- > <a href="files/practical-day2.1.3.pdf">practical
-2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version with all
-commands</a>]<br>
- > <a href="files/practical-day3.1.2.pdf">practical
-3</a><br>
-<br>
-- MRC methodological session: Introduction to phylogenetics:<br>
- > <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
- > <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
- > data (<a href="files/usflu.fasta">DNA sequences</a>,
-<a href="files/usflu.annot.csv">annotations</a>)<br>
-- Imperial College - MSc '<span style="font-style: italic;">Modern
-Epidemiology</span>': <span style="font-weight: bold;">Introduction to
-phylogenetics</span>.<br>
- > <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
- > data (<a href="files/usflu.fasta">usflu.fasta</a>,
-<a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
-<br>
-<br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing lists
-archives </span><br>
-Use the <a target="_top" href="search.html">search engine</a> to
-browse the <span style="font-weight: bold;">archives</span> of the <span
- style="font-weight: bold;">adegenet forum</span>.<br>
-See the '<a href="contact.html">contact</a>' section of this website
-for further information on mailing lists.<br>
-<br>
-<br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);">Miscellaneous<br>
-</span>- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
-
-the
-list of <span style="font-weight: bold;">functions</span> working <span
- style="font-weight: bold;">only for diploid</span> genotypes <br>
-<br>
-<br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);"></span><br>
-<span style="text-decoration: underline;"></span><br>
-<span style="color: rgb(255, 0, 0);"></span></div>
-</body>
+ </head>
+ <body>
+ <br>
+ <br>
+ <br>
+ <div style="margin-left: 40px;">As a <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, each component of adegenet is documented in help pages.
+ As a
+ starting point, one can type <span style="font-family: monospace;
+ font-weight: bold;">?adegenet</span> in
+ R to get an overview of package. Other sources of information
+ distributed with the package include a manual and vignettes. This
+ website also provides other resources such as lectures and
+ practicals.<br>
+ <br>
+ <span style="font-weight: bold;">To search quickly</span> through
+ these
+ resources, use the <a target="_top" href="search.html">search
+ engine</a>. <br>
+ <br>
+ <br>
+ <br>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);">Manuals</span><br>
+ - the adegenet <span style="font-weight: bold;">manual</span> (<a
+ href="files/adegenet-manual.pdf">pdf</a>), which compiles all
+ the
+ manpages of the package.<br>
+ <br>
+ <br>
+ <span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
+ vignettes </span><br>
+ - <a href="files/adegenet-basics.pdf"><span style="font-style:
+ italic;">adegenet-basics</span></a>:
+ introduction
+ to the package; accessible from R by typing <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-basics")</span>.<br>
+ </div>
+ - <a
+ href="files/adegenet-spca.pdf"><span style="font-style: italic;">adegenet-spca</span></a>:
+ spatial
+ multivariate analysis using adegenet; includes an introduction
+ to spatial PCA (sPCA); accessible from R by typing <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-spca")</span>.<br>
+ <div style="margin-left: 40px;">- <a href="files/adegenet-dapc.pdf"><span
+ style="font-style: italic;">adegenet-dapc</span></a>: analysis
+ of the
+ genetic structuring of populations; includes an introduction to
+ Discriminant Analysis of Principal Components (DAPC); accessible
+ from R
+ by typing <span style="font-family: monospace; color: rgb(255, 0,
+ 0);">vignette("adegenet-dapc")</span>.<br>
+ - <a href="files/adegenet-genomics.pdf"><span style="font-style:
+ italic;">adegenet-genomics</span></a>: introduction
+ to the handling of genome-wide SNP data using adegenet; accessible
+ from
+ R by typing <span style="font-family: monospace; color: rgb(255,
+ 0, 0);">vignette("adegenet-genomics")</span>.<br>
+ <br>
+ <br>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);">Lectures
+ and
+ practicals</span><br>
+ - globaldiv summer school 2009, Piacenza, Italie: <a
+ href="files/globaldiv-TJ.1.3.pdf">talk</a> - <a
+ href="files/globaldiv-PC.1.3.pdf">practical course</a><br>
+ <br>
+ - Master 2 "Ecology, Evolution, Biometry", Lyon, France: <a
+ href="files/talk-E2B.1.0.pdf">talk</a> - <a
+ href="files/TD-E2B.pdf">practical
+ course</a><br>
+ <br>
+ - One-week course on Genetic Data Analysis, Bogota, Colombia: <br>
+ > <a href="files/day1.1.2.pdf">lecture 1</a>:
+ methodological overview<br>
+ > <a href="files/day2.1.3.pdf">lecture 2</a>:
+ finding clusters, using cluster information<br>
+ > <a href="files/day3.1.2.pdf">lecture 3</a>:
+ spatial genetics<br>
+ > <a href="files/practical-day1.1.2.pdf">practical
+ 1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
+ with all
+ commands</a>]<br>
+ > <a href="files/practical-day2.1.3.pdf">practical
+ 2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
+ with all
+ commands</a>]<br>
+ > <a href="files/practical-day3.1.2.pdf">practical
+ 3</a><br>
+ <br>
+ - MRC methodological session: Introduction to phylogenetics:<br>
+ > <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
+ > <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
+ > data (<a href="files/usflu.fasta">DNA
+ sequences</a>,
+ <a href="files/usflu.annot.csv">annotations</a>)<br>
+ <br>
+ - Imperial College - MSc "<span style="font-style: italic;">Modern
+ Epidemiology</span>": <span style="font-weight: bold;">Introduction
+ to
+ phylogenetics</span>.<br>
+ > <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
+ > data (<a href="files/usflu.fasta">usflu.fasta</a>,
+ <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
+ <br>
+ - RAPID-NGS workshop, Münster (March 2013) - <span
+ style="font-weight: bold;">Outbreak analysis using <span
+ style="font-style: italic;">adegenet </span>and <span
+ style="font-style: italic;">ape</span></span> <img
+ style="width: 80px; height: 37px;" alt="new"
+ src="images/new.png"><br>
+ > <a
+ href="files/seqTrack-practical.1.2.pdf">practical</a><br>
+ > data (<a
+ href="files/fakeOutbreak/cases.csv">cases.csv</a>, <a
+ href="files/fakeOutbreak/alignment.fa">alignment.fa</a>, <a
+ href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
+ <br>
+ <br>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing
+ lists
+ archives </span><br>
+ Use the <a target="_top" href="search.html">search engine</a> to
+ browse the <span style="font-weight: bold;">archives</span> of
+ the <span style="font-weight: bold;">adegenet forum</span>.<br>
+ See the '<a href="contact.html">contact</a>' section of this
+ website
+ for further information on mailing lists.<br>
+ <br>
+ <br>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);">Miscellaneous<br>
+ </span>- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
+ the
+ list of <span style="font-weight: bold;">functions</span> working
+ <span style="font-weight: bold;">only for diploid</span> genotypes
+ <br>
+ <br>
+ <br>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);"></span><br>
+ <span style="text-decoration: underline;"></span><br>
+ <span style="color: rgb(255, 0, 0);"></span></div>
+ </body>
</html>
Added: www/files/seqTrack-practical.1.2.pdf
===================================================================
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+F
[TRUNCATED]
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svnlook diff /svnroot/adegenet -r 1080
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