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---
layout: workshop # DON'T CHANGE THIS.
root: . # DON'T CHANGE THIS.
venue: "RNAseq analysis in R" # brief name of host site without address (e.g., "Euphoric State University")
address: "Rm 329, Maths and Physics Building, Sandy Bay Campus, University of Tasmania" # street address of workshop (e.g., "123 Forth Street, Blimingen, Euphoria")
country: "au" # country (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en" # language (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "-42.903804,147.326509" # fractional latitude and longitude (e.g., "41.7901128,-87.6007318"; you can use http://www.latlong.net/)
humandate: "Nov 24-25, 2016" # human-readable date (e.g., "Feb 17-18, 2020")
humantime: "9:00 am - 5:00 pm" # human-readable time (e.g., "9:00 am - 4:30 pm")
startdate: 2016-11-24 # use YYYY-MM-DD format like 2015-01-01
enddate: 2016-11-25 # use YYYY-MM-DD format like 2015-01-02
instructor: ["Matt Ritchie", "Charity Law"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Andrew Phipps", "Valerie Hecht"]
contact: "combine@combine.org.au" # contact email address for workshop organizer, such as "grace@hopper.org"
etherpad: http://pad.software-carpentry.org/2016-11-24-RNAseq
eventbrite: # optional (insert the alphanumeric key for Eventbrite registration, e.g., "1234567890AB")
---
<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->
<!--
HEADER
Edit the values in the block above to be appropriate for your workshop.
If the value is not 'true', 'false', 'null', or a number, please use
double quotation marks around the value, unless specified otherwise.
And run 'tools/check' *before* committing to make sure that changes are good.
-->
<!--
EVENTBRITE
This block includes the Eventbrite registration widget if
'eventbrite' has been set in the header. You can delete it if you
are not using Eventbrite, or leave it in, since it will not be
displayed if the 'eventbrite' field in the header is not set.
-->
{% if page.eventbrite %}
<iframe
src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
frameborder="0"
width="100%"
height="248px"
scrolling="auto">
</iframe>
{% endif %}
<p>
<a href="https://combine.org.au/" title="COMBINE">
<img alt="COMBINE" src="https://combineau.files.wordpress.com/2016/03/combine_logo_2016_draft_v5.png" height="180" />
</a>
</p>
<br>
<p>
<strong>Sponsors:</strong>
</p>
<p>
<a href="http://www.agtagenomics.org.au/">
<img border="0" alt="AGTA" src="https://combineau.files.wordpress.com/2015/05/agta-logo.jpg" height="100">
</a>
<a href="http://www.vlsci.org.au/">
<img border="0" alt="VLSCI" src="https://combineau.files.wordpress.com/2015/05/logo_vlsci_rgb.jpg" height="100">
</a>
</p>
<h2 id="general">General Information</h2>
<!--
INTRODUCTION
Edit the general explanatory paragraph below if you want to change
the pitch.
-->
<p>
In this workshop, you will be learning how to analyse RNA-seq count data, using
R. This will include reading the data into R, quality control and performing
differential expression analysis and gene set testing, with a focus on the
limma-voom analysis workflow. You will learn how to generate common plots for
analysis and visualisation of gene expression data, such as boxplots and
heatmaps. This workshop is aimed at biologists interested in learning how to
perform differential expression analysis of RNA-seq data when reference genomes
are available.
</p>
<!--
AUDIENCE
Explain who your audience is. (In particular, tell readers if the
workshop is only open to people from a particular institution.
-->
<p id="who">
<strong>Who:</strong>
The course is aimed at graduate students and other researchers.
<strong>Some basic R knowledge is assumed</strong>.
This is not an introduction to R course.
If you are not familiar with the R statistical programming language we
strongly encourage you to work through an introductory R course before you
attend this workshop. We recommend the Software Carpentry
<a href="http://swcarpentry.github.io/r-novice-gapminder/">R for Reproducible Scientific Analysis</a>
lessons up to and including vectorisation (topic 9).
</p>
<!--
LOCATION
This block displays the address and links to maps showing directions
if the latitude and longitude of the workshop have been set. You
can use http://itouchmap.com/latlong.html to find the lat/long of an
address.
-->
{% if page.latlng %}
<p id="where">
<strong>Where:</strong>
{{page.address}}.
Get directions with
<a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
or
<a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}
<!--
SPECIAL REQUIREMENTS
Modify the block below if there are any special requirements.
-->
<p id="requirements">
<strong>Requirements:</strong> Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
<a href="#setup">below</a>).
</p>
<!--
CONTACT EMAIL ADDRESS
Display the contact email address set in the header. If an address
isn't set in the header, the Software Carpentry admin address is
used.
-->
<p>
<strong>Organisers</strong>:
Michael Charleston (<a href='michael.charleston@utas.edu.au'>michael.charleston@utas.edu.au</a>) and
Andrew Phipps (<a href='andrew.phipps@utas.edu.au'>andrew.phipps@utas.edu.au</a>).
</p>
<p id="contact">
<strong>Contact</strong>:
Please mail
{% if page.contact %}
<a href='mailto:{{page.contact}}'>{{page.contact}}</a>
{% else %}
<a href='mailto:{{site.contact}}'>{{site.contact}}</a>
{% endif %}
for more information.
</p>
<p>
<strong>Registration:</strong> register
<a href="https://goo.gl/forms/ADNd2gf49YPQl5Gv2">here</a>.
Registration is $50 for students, and $60 for non-students.
</p>
<hr/>
<!--
SCHEDULE
Show the workshop's schedule. Edit the items and times in the table
to match your plans. You may also want to change 'Day 1' and 'Day
2' to be actual dates or days of the week.
-->
<h2 id="schedule">Schedule</h2>
<!-- DO NOT EDIT SURVEY LINKS -->
<!--
<p><em>Surveys</em></p>
<p>Please be sure to complete the survey after the workshop. Link to be provided later.</p>
-->
<!--
<p><a href='{{ site.swc_pre_survey }}{{ site.github.project_title }}'>Pre-workshop Survey</a></p>
<p><a href='{{ site.swc_post_survey }}{{ site.github.project_title }}'>Post-workshop Survey</a></p>
-->
<p>
</p>
<p>
Note: this is a preliminary schedule. There may be changes to the timing and content.
</p>
<p>
If you have any trouble installing the software or packages, please arrive
at 9am on the first day so we can help before the workshop starts.
</p>
<div class="row">
<div class="col-md-6">
<h3>Day 1</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Installation and set up</td> </tr>
<tr> <td>09:30</td> <td>Introduction to RNA-seq theory</td> </tr>
<tr> <td>10:15</td> <td>R for RNAseq</tr>
<tr> <td>11:00</td> <td><i>Break</i></td> </tr>
<tr> <td>11:30</td> <td>Quality control and visualisation</tr>
<tr> <td>12:30</td> <td><i>Lunch</i></td> </tr>
<tr> <td>13:30</td> <td>Quality control and visualisation continued</td> </tr>
<tr> <td>15:00</td> <td><i>Break</i></td> </tr>
<tr> <td>15:30</td> <td>Quality control and visualisation continued</td> </tr>
<tr> <td>17:00</td> <td><i>Wrap-up</i></td> </tr>
</table>
</div>
<div class="col-md-6">
<h3>Day 2</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Differential expression theory</td> </tr>
<tr> <td>09:45</td> <td>Differential expression analysis</td> </tr>
<tr> <td>11:00</td> <td><i>Break</i></td> </tr>
<tr> <td>11:30</td> <td>Differential expression analysis continued</td> </tr>
<tr> <td>12:30</td> <td><i>Lunch</i></td> </tr>
<tr> <td>13:30</td> <td>Differential expression analysis continued</td> </tr>
<tr> <td>15:00</td> <td><i>Break</i></td> </tr>
<tr> <td>15:30</td> <td>Gene set testing</td> </tr>
<tr> <td>17:00</td> <td><i>Wrap-up</i></td> </tr>
</table>
</div>
</div>
<!--
ETHERPAD
At `_misc/etherpad.txt` you will find a template for the etherpad.
Display the Etherpad for the workshop. You can set this up in
advance or on the first day; either way, make sure you push changes
to GitHub after you have its URL. To create an Etherpad, go to
http://pad.software-carpentry.org/YYYY-MM-DD-site
where 'YYYY-MM-DD-site' is the identifier for your workshop,
e.g., '2015-06-10-esu'.
-->
{% if page.etherpad %}
<p id="etherpad">
<strong>Etherpad:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
<br/>
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
</p>
{% endif %}
<hr/>
<!--
SYLLABUS
Show what topics will be covered.
-->
<h2 id="syllabus">Syllabus</h2>
You can find all of the lesson notes for this workshop
<a href="http://combine-australia.github.io/RNAseq-R/">here</a>.
<hr/>
<!--
SETUP
Delete irrelevant sections from the setup instructions. Each
section is inside a 'div' without any classes to make the beginning
and end easier to find.
This is the other place where people frequently make mistakes, so
please preview your site before committing, and make sure to run
'tools/check' as well.
-->
<h2 id="data">Data</h2>
<p>
Please download these data files and save them to your laptop before the workshop:
<ul>
<li>Mouse mammary data (counts): <a href="https://figshare.com/s/1d788fd384d33e913a2a" class="uri">https://figshare.com/s/1d788fd384d33e913a2a</a></li>
</ul>
</p>
<h2 id="setup">Setup</h2>
<p>
To participate in this workshop, you will need
access to the software described below. In addition, you will
need an up-to-date web browser.
</p>
<p>
Even if you already have R installed, it is important that you have the latest
version because some of the packages we will be using will not work with earlier
versions of R. The latest version (available through the links below) is 3.3.1.
For Mac 10.6-10.8 the latest version is 3.2.1 (available from
<a href = "https://cran.r-project.org/bin/macosx/">here</a>)
and for that version you will also need to download this gfortran package
<a href = "https://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg">gfortran package</a>).
</p>
<p>
Software Carpentry maintains a list of common issues that occur during installation as a reference for instructors
that may be useful on the
<a href = "https://github.com/swcarpentry/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
</p>
<div id="r"> <!-- Start of 'R' section. -->
<h3>R</h3>
<p>
<a href="http://www.r-project.org">R</a> is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R, we use
<a href="http://www.rstudio.com/">RStudio</a>.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="r-windows">Windows</h4>
<a href="https://www.youtube.com/watch?v=q0PjTAylwoU">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="http://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
from <a href="http://cran.r-project.org/index.html">CRAN</a>.
</p>
<p>
Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="r-macosx">Mac OS X</h4>
<a href="https://www.youtube.com/watch?v=5-ly3kyxwEg">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="http://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
from <a href="http://cran.r-project.org/index.html">CRAN</a>.
</p>
<p>
Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="r-linux">Linux</h4>
<p>
You can download the binary files for your distribution
from <a href="http://cran.r-project.org/index.html">CRAN</a>. Or
you can use your package manager (e.g. for Debian/Ubuntu
run <code>sudo apt-get install r-base</code> and for Fedora run
<code>sudo yum install R</code>).
</p>
<p>
Also, please install the
<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
</p>
</div>
</div>
<h4>R packages</h4>
<p>
You will also need to install the following R packages:
<strong>limma, edgeR, gplots, org.Mm.eg.db, org.Dm.eg.db, RColorBrewer, GO.db, BiasedUrn, DESeq2, Glimma</strong>.
</p>
<p>
If you are bringing your own data to analyse on Day 2, you should also install the annotation package for your species.
To find the name of the package you will need, look on the
<a href="http://bioconductor.org/packages/3.3/BiocViews.html#___AnnotationData">Bioconductor website</a>
(Search for "org." to see the organism packages).
</p>
<p>
These can all be obtained from <a href="https://www.bioconductor.org/">Bioconductor</a>.
</p>
<p>
Open RStudio and run the following commands to install packages from Bioconductor:
</p>
<p>
<code>> source("http://bioconductor.org/biocLite.R")</code>
</p>
<p>
<code>> biocLite("limma")</code>
</p>
<p>
Repeat this for each package.
</p>
<p>
<code>> biocLite("edgeR")</code>
</p>
<p>
<code>…</code>
</p>
<p>
<code>> biocLite("Glimma")</code>
</p>
<p>
Common problems:
<ul>
<li>If the source command doesn't work, try https instead of http.</li>
<li>Make sure you are directly connected to the internet and not using a proxy.</li>
<li>Make sure the package name is in quotes.</li>
</ul>
If you have any trouble please see the
<a href="https://www.bioconductor.org/install/">Instructions for installing Bioconductor packages</a>.
You can also arrive early on the first day of the workshop for help with set up.
</p>
</div> <!-- End of 'R' section. -->