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<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="UTF-8">
<title>Working with Genomic Variants</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="stylesheets/normalize.css" media="screen">
<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
<link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
<link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
</head>
<body>
<section class="page-header">
<h1 class="project-name">Working with Genomic Variants</h1>
<h2 class="project-tagline">Rockefeller University, BRC Course Plotting R</h2>
<a href="https://github.com/rockefelleruniversity/RU_GenomicVariants/zipball/master" class="btn">Download.zip</a>
<a href="https://github.com/rockefelleruniversity/RU_GenomicVariants/tarball/master" class="btn">Download.tar.gz</a>
</section>
<section class="main-content">
<h1>
<a id="Intro_To_R" class="anchor" href="#Intro_To_R" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Working with Genomic Variants</h1>
<p><a href="https://gitter.im/RockefellerUniversity/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge"><img src="https://badges.gitter.im/Join%20Chat.svg" alt="Join the chat at https://gitter.im/RockefellerUniversity/Lobby"></a>
<a href="https://travis-ci.org/RockefellerUniversity/Intro_To_R_1Day"><img src="https://travis-ci.org/RockefellerUniversity/Intro_To_R_1Day.svg?branch=master" alt="https://travis-ci.org/RockefellerUniversity/Intro_To_R_1Day.svg?branch=master"></a>
<a href="https://ci.appveyor.com/project/ThomasCarroll/intro-to-r-1day/branch/master"><img src="https://ci.appveyor.com/api/projects/status/tl4gjj8g8926259g?svg=true
" alt="https://ci.appveyor.com/api/projects/status/tl4gjj8g8926259g?svg=true
"></a>
</p>
<h2>
<a id="the-course" class="anchor" href="#the-course" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>The Course</h2>
<p>This course introduces ChIPseq analysis in Bioconductor.</p>
<p>The course consists of multiple sections, the first section introduces Bioconductor and remaining sections discuss the handling of Genomics data and metadata in R.<br>
Each section is presented as both HTMl and Rpres markdown ( to allow for intergration of the presentation in the RStudio enviroment itself). Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples. </p>
<p>Course material and exercises are available to view as rendered HTML at <a href="https://rockefelleruniversity.github.io/Bioconductor_Introduction/">https://rockefelleruniversity.github.io/Bioconductor_Introduction/</a>.<br>
All material is available to download under GPL v2 license.</p>
<h2>
<a id="setting-up" class="anchor" href="#setting-up" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Setting up.</h2>
<h4>
<a id="install-r" class="anchor" href="#install-r" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install R.</h4>
<p>R can be installed from the R-project website.<br>
R 3.1.0 or higher is required for this course.</p>
<p><a href="http://www.r-project.org/">http://www.r-project.org/</a></p>
<h4>
<a id="install-rstudio" class="anchor" href="#install-rstudio" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install RStudio.</h4>
<p>RStudio can be installed from the R-project website. </p>
<p><a href="http://www.rstudio.com/">http://www.rstudio.com/</a></p>
<h4>
<a id="install-required-packages" class="anchor" href="#install-required-packages" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install required packages.</h4>
<h5><b>Option 1 - (For your own personal computers)</b></h5>
<p>Having downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2).<br>
To install these,</p>
<ul>
<li>First launch RStudio</li>
<li>Install the packages in the R console using devtools
<pre>
install.packages("devtools",dependencies=TRUE)
devtools::install_github("rockefelleruniversity/Bioconductor_Introduction",subdir="BioconductorIntroduction",build_vignettes=TRUE)
</pre>
</li>
</ul>
<h5><b>Option 3 - (For anywhere)</b></h5>
<p>Having downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2).<br>
To install these,</p>
<ul>
<li>First launch RStudio</li>
<li>Install the packages in the R console using install.packages
<pre>
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Mmusculus.UCSC.mm10")
biocLite("BSgenome.Hsapiens.UCSC.hg19")
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
biocLite("TxDb.Mmusculus.UCSC.mm10.knownGene")
biocLite("Org.Mm.eg.db")
biocLite("Org.Hs.eg.db")
biocLite("Biostrings")
biocLite("GenomicRanges")
biocLite("rtracklayer")
</pre>
</li>
</ul>
<h4>
<a id="download-the-material" class="anchor" href="#download-the-material" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Download the material</h4>
<p>The material can either be downloaded as a <a href="https://github.com/rockefelleruniversity/RU_GenomicVariants/archive/master.zip">zip</a></p>
<pre>
wget https://github.com/rockefelleruniversity/RU_GenomicVariants/archive/master.zip ./
</pre>
<h2>
<a id="the-r-sessions" class="anchor" href="#the-r-sessions" aria-hidden="true"><span class="octicon octicon-link"></span></a>Working with Genomic Variants</h2>
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>Working with Genomic Variants</h4>
<p>This section introduces the analysis of Genomic variants in Bioconductor<br>
Session sections:
<ul>
<li>Preprocessing VCF in R</li>
<li>Annotate variants</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/working_with_genomic_variants.html">Working with Genomic Variants</a><br>
Link to single page, printable HTML - <a href="./r_course/working_with_genomic_variants_singlePage.html">Working with Genomic Variants</a><br>
Link to R code included in presentation- - <a href="./r_course/working_with_genomic_variants.R">Working with Genomic Variants</a><br>
<iframe src="./r_course/working_with_genomic_variants.html" width="100%" height="400"></iframe>
<p>
</p>
<!--
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>ChIPseq part2</h4>
<p>This section introduces the analysis of ChIPseq data in Bioconductor<br>
Session sections:
<ul>
<li>Quality control for ChIPseq data in R</li>
<li>Overview of peak calling</li>
<li>Annotation of peaks</li>
</ul>
</p>
Link to HTML presentation - <a href="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor2.html">ChIPseq part2</a><br>
Link to single page, printable HTML - <a href="./chipseq_course/Presentations/singlepage/ChIPseq_In_Bioconductor2.html">ChIPseq part2</a><br>
Link to R code included in presentation- - <a href="./r_course/presentations/rcode/ChIPseq_In_Bioconductor2.R">ChIPseq part2</a><br>
<iframe src="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor2.html" width="100%" height="400"></iframe>
<p>
</p>
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>ChIPseq part3</h4>
<p>This section introduces the analysis of ChIPseq data in Bioconductor<br>
Session sections:
<ul>
<li>Functional enrichment analysis of TF targets</li>
<li>R interface to GREAT server</li>
<li>Motif enrichment using Meme-ChIP</li>
</ul>
</p>
Link to HTML presentation - <a href="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor3.html">ChIPseq part3</a><br>
Link to single page, printable HTML - <a href="./chipseq_course/Presentations/singlepage/ChIPseq_In_Bioconductor3.html">ChIPseq part3</a><br>
Link to R code included in presentation- - <a href="./r_course/presentations/rcode/ChIPseq_In_Bioconductor3.R">ChIPseq part3</a><br>
<iframe src="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor3.html" width="100%" height="400"></iframe>
<p>
</p>
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>ChIPseq part4</h4>
<p>This section introduces the analysis of ChIPseq data in Bioconductor<br>
Session sections:
<ul>
<li>Identification of replicated, high confidence peaks</li>
<li>Finding peaks unique and common to conditions</li>
<li>Differential ChIP-seq</li>
</ul>
</p>
Link to HTML presentation - <a href="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor4.html">ChIPseq part4</a><br>
Link to single page, printable HTML - <a href="./chipseq_course/Presentations/singlepage/ChIPseq_In_Bioconductor4.html">ChIPseq part4</a><br>
Link to R code included in presentation- - <a href="./r_course/presentations/rcode/ChIPseq_In_Bioconductor4.R">ChIPseq part4</a><br>
<iframe src="./chipseq_course/Presentations/Slides/ChIPseq_In_Bioconductor4.html" width="100%" height="400"></iframe>
<p>
</p>
-->
</span>
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