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<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="UTF-8">
<title>An Intro to Bioconductor by BRC</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">Bioconductor Introduction</h1>
<h2 class="project-tagline">Rockefeller University, BRC Course</h2>
<a href="https://github.com/rockefelleruniversity/Bioconductor_Introduction/zipball/master" class="btn">Download.zip</a>
<a href="https://github.com/rockefelleruniversity/Bioconductor_Introduction/tarball/master" class="btn">Download.tar.gz</a>
<a href="https://github.com/RockefellerUniversity/Bioconductor_Introduction/issues" class="btn">Getting help !</a>
</section>
<section class="main-content">
<h1>
<a id="Intro_To_Bioconductor" class="anchor" href="#Intro_To_R" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Introduction to Bioconductor</h1>
<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 the Bioconductor set of R packages.</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 using Bioconductor packages.<br>
Each section is presented as HTMl presentations or single page document. 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 3.6.0 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 (Bioconductor packages).<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 2 - For anywhere</b></h5>
<p>Having downloaded R and RStudio, some additional packages are required (Bioconductor packages).<br>
To install these,</p>
<ul>
<li>First launch RStudio</li>
<li>Install Bioconductor. Version 3.10 or higher is required for this course. Then install Bioconductor packages in the R console using BiocManager::install()
<pre>
BiocManager::install(version = "3.10")
BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
BiocManager::install("Org.Mm.eg.db")
BiocManager::install("Org.Hs.eg.db")
BiocManager::install("Biostrings")
BiocManager::install("GenomicRanges")
BiocManager::install("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/Bioconductor_Introduction/archive/master.zip">zip</a></p>
<pre>
wget https://github.com/rockefelleruniversity/Bioconductor_Introduction/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>Introduction to Bioconductor</h2>
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to Bioconductor</h4>
<p>This section introduces the Bioconductor set of R packages.<br>
Session sections:
<ul>
<li>Bioconductor overview</li>
<li>Packages for Genomics data</li>
<li>Package installation</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/bioconductor_introduction.html">Session 1</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/bioconductor_introduction.html">Session 1</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/bioconductor_introduction.R">Session 1</a><br>
<iframe src="./r_course/presentations/slides/bioconductor_introduction.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session2" class="anchor" href="#session2" aria-hidden="true"><span class="octicon octicon-link"></span></a>Sequences in Bioconductor</h4>
<p>In this session we introduce genomic sequence handling and import/export<br>
Session sections:
<ul>
<li>Introduction to BSgenome packages</li>
<li>Manipulating sequence data using Biostrings package</li>
<li>Export/Import of FASTA files</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/SequencesInBioconductor.html">Session 2</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/SequencesInBioconductor.html">Session 2</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/SequencesInBioconductor.R">Session 2</a><br>
<iframe src="./r_course/presentations/slides/SequencesInBioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session3" class="anchor" href="#session3" aria-hidden="true"><span class="octicon octicon-link"></span></a>Genomic Intervals in Bioconductor</h4>
<p>In this session we introduce genomic interval handling and import/export<br>
Session sections:
<ul>
<li>Introduction to GenomicRanges packages</li>
<li>Manipulating genomic intervals</li>
<li>Export/Import of BED files</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/GenomicIntervals_In_Bioconductor.html">Session 3</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/GenomicIntervals_In_Bioconductor.html">Session 3</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/GenomicIntervals_In_Bioconductor.R">Session 3</a><br>
<iframe src="./r_course/presentations/slides/GenomicIntervals_In_Bioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session4" class="anchor" href="#session4" aria-hidden="true"><span class="octicon octicon-link"></span></a>Genomic Scores in Bioconductor</h4>
<p>In this session we introduce genomic scores handling and import/export<br>
Session sections:
<ul>
<li>Importing and exporting bedGraph and bigWig files</li>
<li>Manipulating genomic scores in R</li>
<li>Operations and summary statitics using genomic scores</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/GenomicScores_In_Bioconductor.html">Session 4</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/GenomicScores_In_Bioconductor.html">Session 4</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/GenomicScores_In_Bioconductor.R">Session 4</a><br>
<iframe src="./r_course/presentations/slides/GenomicScores_In_Bioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session5" class="anchor" href="#session5" aria-hidden="true"><span class="octicon octicon-link"></span></a>Genomic Features in Bioconductor</h4>
<p>In this session we introduce genomic scores handling and import/export<br>
Session sections:
<ul>
<li>Importing and exporting Gene models as GTF/GFF</li>
<li>Working with TxDb objects</li>
<li>Retrieving annotation from OrgDb packages</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/GenomicFeatures_In_Bioconductor.html">Session 5</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/GenomicFeatures_In_Bioconductor.html">Session 5</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/GenomicFeatures_In_Bioconductor.R">Session 5</a><br>
<iframe src="./r_course/presentations/slides/GenomicFeatures_In_Bioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session6" class="anchor" href="#session6" aria-hidden="true"><span class="octicon octicon-link"></span></a>FastQs in Bioconductor</h4>
<p>In this session we introduce FastQ handling and import/export<br>
Session sections:
<ul>
<li>Importing and exporting FastQ files</li>
<li>Quality assessment of FastQ files</li>
<li>Trimming and duplicate removal</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/FastQInBioconductor.html">Session 6</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/FastQInBioconductor.html">Session 6</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/FastQInBioconductor.R">Session 6</a><br>
<iframe src="./r_course/presentations/slides/FastQInBioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session7" class="anchor" href="#session7" aria-hidden="true"><span class="octicon octicon-link"></span></a>Alignment in Bioconductor</h4>
<p>In this session we introduce alignment in Bioconductor<br>
Session sections:
<ul>
<li>Genomic and Splice aware alignment</li>
<li>QuasR, Rbowtie2 and Rsubread packages</li>
<li>Sorting and indexing BAM files</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/AlignmentInBioconductor.html">Session 7</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/AlignmentInBioconductor.html">Session 7</a><br>
Link to R codes included in presentation - <a href="./r_course/presentations/r_code/AlignmentInBioconductor.R">Session 7</a><br>
<iframe src="./r_course/presentations/slides/AlignmentInBioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session8" class="anchor" href="#session8" aria-hidden="true"><span class="octicon octicon-link"></span></a>Aligned data in Bioconductor</h4>
<p>In this session we introduce aligned data in Bioconductor<br>
Session sections:
<ul>
<li>Import and export of BAM files</li>
<li>Reads as GAlignment objects</li>
<li>Conversion between GAlignment and GRanges objects</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/AlignedDataInBioconductor.html">Session 8</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/AlignedDataInBioconductor.html">Session 8</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/AlignedDataInBioconductor.R">Session 8</a><br>
<iframe src="./r_course/presentations/slides/AlignedDataInBioconductor.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session9" class="anchor" href="#session9" aria-hidden="true"><span class="octicon octicon-link"></span></a>Summarizing aligned data in Bioconductor</h4>
<p>In this session we introduce summarization of aligned data in Bioconductor<br>
Session sections:
<ul>
<li>Creating coverage from BAM</li>
<li>Counting reads in regions</li>
<li>Summarising counts from large BAM files</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/Summarising_Scores_In_Bioconductor.html">Session 9</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/Summarising_Scores_In_Bioconductor.html">Session 9</a><br>
Link to R code included in presentation - <a href="./r_course/presentations/r_code/Summarising_Scores_In_Bioconductor.R">Session 9</a><br>
<iframe src="./r_course/presentations/slides/Summarising_Scores_In_Bioconductor.html" width="100%" height="400"></iframe>
</span>
<p>
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