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<h1 class="title toc-ignore">All the Resources!</h1>
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<div id="reading-about-good-code-in-general" class="section level2">
<h2>Reading about good code in general</h2>
<ul>
<li>For tips for writing good code and creating reproducible projects: <a href="https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/">Reproducibility in Cancer Informatics</a></li>
<li>For tips for writing pull requests: <a href="https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/engaging-in-code-review---as-an-author.html">Engaging in Code Review as an Author</a> by Candace Savonen.</li>
<li>For tips for reviewing pull requests: <a href="https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/engaging-in-code-review---as-a-reviewer.html">Engaging in Code Review as an Reviewer</a> by Candace Savonen.</li>
<li>For more on effective code review: <a href="https://www.freecodecamp.org/news/a-zen-manifesto-for-effective-code-reviews-e30b5c95204a/">A zen manifesto for effective code reviews</a> by Jean-Charles Fabre.</li>
<li>About <a href="https://github.com/AlexsLemonade/training-modules/blob/master/intro-to-R-tidyverse/00c-good-scientific-coding-practices.md">Good scientific coding practices</a> by the Childhood Cancer Data Lab.</li>
<li><a href="https://github.com/AlexsLemonade/training-modules/blob/master/intro-to-R-tidyverse/00b-debugging_resources.md">Tips for debugging code from the Childhood Cancer Data Lab</a></li>
<li>For good practices on code review: <a href="https://smartbear.com/en/learn/code-review/best-practices-for-peer-code-review/">Best practices for Code Review</a> from SmartBear.</li>
</ul>
</div>
<div id="training-networks" class="section level2">
<h2>Training Networks</h2>
<p>These places have workshops, online and in person groups, and/or tutorials that can help you get plugged into training opportunities and connect others who are learning informatics.</p>
<ul>
<li><a href="https://www.itcrtraining.org/">ITCR Training Network</a> - hosts events, workshops and creates content for cancer informatics.</li>
<li><a href="https://carpentries.org">The Carpentries</a>, with lessons from <a href="https://datacarpentry.org">Data Carpentry</a> and <a href="https://software-carpentry.org/lessons/">Software Carpentry</a></li>
<li><a href="https://www.ccdatalab.org/">Childhood Cancer Data Lab</a> - more specific to childhood cancer research. Has great workshops, materials, and software tools.</li>
<li><a href="https://www.genepattern.org/">Gene Pattern</a> - has an online ‘point and click’ website with a large library of tutorials to reference. They also host workshops.</li>
<li><a href="https://training.galaxyproject.org/">Galaxy Training Network</a> - has an online server you can work from and lots of tutorials for different data types.</li>
<li><a href="https://meetings.cshl.edu/courseshome.aspx">Cold Spring Harbor</a> offers a variety of courses for genomics.</li>
<li>If you specifically work on Childhood Cancer Research, we recommend getting plugged in with the <a href="https://www.ccdatalab.org/">Childhood Cancer Data Lab</a>. They have workshops and their own Slack tailored to the specifics of childhood cancer data science research.</li>
</ul>
</div>
<div id="groups-for-discussing-code" class="section level2">
<h2>Groups for discussing code</h2>
<p>These are completely free groups that you can join anytime that are also filled with people also tackling coding and informatics research.</p>
<ul>
<li><a href="https://rladies.org/"><strong>R Ladies</strong></a>: A group that has local meetups to discuss R and R topics. (Not exclusive to women-identifying individuals). See here for the <a href="https://www.meetup.com/rladies-seattle/">R Ladies Seattle</a>.</li>
<li><a href="https://app.slack.com/client/T8NN74686"><strong>Fred Hutch Slack R User Group</strong></a>: Discusses programming, data analysis, and troubleshooting in R for users of a wide range of expertise and research topic, as well as tools based in R such as Shiny applications. See the #r-user-comm channel on <a href="https://app.slack.com/client/T8NN74686">FH-BCR Slack</a> for more information. Currently an online Slack channel only.</li>
<li><a href="https://app.slack.com/client/T8NN74686"><strong>Fred Hutch Slack Python User Group</strong></a>: Discusses programming, data analysis, and troubleshooting in Python and related topics in general software development. See the #python-user-comm channel on <a href="https://app.slack.com/client/T8NN74686">FH-BCR Slack</a> for more information. Currently an online Slack channel only.</li>
<li>The <a href="https://www.ccdatalab.org/">Childhood Cancer Data Lab</a> has their own Slack tailored to the specifics of childhood cancer data science research.</li>
</ul>
</div>
<div id="free-online-resources" class="section level2">
<h2>Free online resources</h2>
<p>There are a lot of resources online that you can work through at your own pace. Most are completely free. If they are not free, this is noted in the list.</p>
<div id="r-and-tidyverse" class="section level3">
<h3>R and Tidyverse</h3>
<ul>
<li><a href="https://swirlstats.com/">Swirl, an interactive tutorial</a><br />
</li>
<li><a href="https://r4ds.had.co.nz/">R for Data Science</a><br />
</li>
<li><a href="http://jhudatascience.org/tidyversecourse/">Tidyverse skills for Data Science</a> by Carrie Wright.</li>
<li><a href="https://www.rstudio.com/resources/cheatsheets/">Handy R cheatsheets</a><br />
</li>
<li><a href="https://rc2e.com/">R Cookbook Second Edition</a></li>
<li><a href="https://adv-r.hadley.nz/">Advanced R</a></li>
<li><a href="https://www.r4epi.com/">R for Epidemiology</a> - has generally good R advice</li>
<li><a href="https://www.spl.org/books-and-media/books-and-ebooks/safari-books-online">O’Reilly books</a> available through Seattle Public Library</li>
</ul>
</div>
<div id="r-notebooks" class="section level3">
<h3>R notebooks</h3>
<ul>
<li><a href="http://rmarkdown.rstudio.com">R Markdown</a><br />
</li>
<li><a href="https://ismayc.github.io/rbasics-book/">Tutorial on R, RStudio and R Markdown</a></li>
<li><a href="https://www.rstudio.com/resources/cheatsheets/">Handy R cheatsheets</a><br />
</li>
<li><a href="https://bookdown.org/yihui/rmarkdown/">R Notebooks tutorial</a></li>
</ul>
</div>
<div id="r-and-genomics" class="section level3">
<h3>R and Genomics</h3>
<ul>
<li><a href="https://github.com/AlexsLemonade/training-modules/tree/master/intro-to-R-tidyverse">Intro to R and Tidyverse course and exercises</a> from the Childhood Cancer Data Lab.</li>
<li><a href="https://alexslemonade.github.io/refinebio-examples/index.html">Refine.bio examples</a> from the Childhood Cancer Data Lab.</li>
<li><a href="https://www.biostarhandbook.com">Biostar Handbook: A Beginner’s Guide to Bioinformatics</a></li>
</ul>
</div>
<div id="python" class="section level3">
<h3>Python</h3>
<ul>
<li><a href="https://jakevdp.github.io/PythonDataScienceHandbook/">Python Data Science Handbook</a></li>
<li><a href="https://www.pythonforbiologists.org/">Python for Biologists</a></li>
</ul>
</div>
</div>
<div id="learn-on-your-own-courses" class="section level2">
<h2>Learn on your own courses</h2>
<p>If you want to learn on your own, but would like a more formal course set up and schedule, these courses can offer you more structure as well as certification.</p>
<div id="itn-courses-and-course-material" class="section level3">
<h3>ITN Courses and course material</h3>
<p>See the <a href="https://www.itcrtraining.org/courses">full listing of ITN courses here</a>.</p>
<ul>
<li><strong>Introduction to Reproducibility in Cancer Informatics</strong> - a hands-on course that takes you through good practices for creating reproducible data analyses. Can be be followed along using R or Python.
<ul>
<li>The material for this course can be viewed without login requirement on this <a href="https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/">Bookdown website</a>. This format might be most appropriate for you if you rely on screen-reader technology.</li>
<li>This course can be taken for <a href="https://leanpub.com/universities/courses/jhu/intro-reproducibility-in-cancer-informatics">free certification through Leanpub</a>.</li>
<li>This course can be taken on <a href="https://www.coursera.org/learn/intro-to-reproducibility-cancer-informatics">Coursera for certification here</a> (but it is not available for free on Coursera).</li>
</ul></li>
<li><strong>Advanced Reproducibility for Cancer Informatics</strong> - the sequel course to the Intro to Reproducibility course.
<ul>
<li>The material for this course can be viewed without login requirement on this <a href="https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/">Bookdown website</a>. This format might be most appropriate for you if you rely on screen-reader technology.</li>
<li>This course can be taken for <a href="https://leanpub.com/universities/courses/jhu/adv-reproducibility-in-cancer-informatics">free certification through Leanpub</a>.</li>
<li>This course can be taken on <a href="https://www.coursera.org/learn/adv-reproducibility-cancer-informatics">Coursera for certification here</a> (but it is not available for free on Coursera).</li>
</ul></li>
<li><strong>Documentation and Usability in Cancer Informatics</strong> - Discusses best practices for creating usable software and thorough documentation.
<ul>
<li>The material for this course can be viewed without login requirement on this <a href="https://jhudatascience.org/Documentation_and_Usability">Bookdown website</a>. This format might be most appropriate for you if you rely on screen-reader technology.</li>
<li>This course can be taken for <a href="https://leanpub.com/universities/courses/jhu/documentation_and_usability/">free certification through Leanpub</a>.</li>
<li>This course can be taken on <a href="https://www.coursera.org/learn/documentation-usability-cancer-informatics">Coursera for certification here</a> (but it is not available for free on Coursera).</li>
</ul></li>
</ul>
</div>
<div id="other-online-courses" class="section level3">
<h3>Other online courses</h3>
<ul>
<li><a href="https://github.com/fredhutchio/tfcb_2019">MCB517A: Tools for Computational Biology</a>: A graduate-level course taught for UW by Fred Hutch CompBio faculty. This links to a GitHub repository that includes all lectures and homework.
<ul>
<li><a href="https://github.com/fredhutchio/tfcb_2019/tree/master/software">How to install necessary software for this course</a></li>
<li><a href="https://github.com/fredhutchio/tfcb_2019/issues">Ask questions about this course</a></li>
<li><em>Course materials all available for free</em></li>
</ul></li>
<li><a href="https://www.edx.org">edX</a>: Offers a collection of courses for <a href="https://www.edx.org/course/subject/data-analysis-statistics">Data Analysis and Statistics</a> and <a href="https://www.edx.org/learn/bioinformatics">Bioinformatics</a>
<ul>
<li><a href="http://rafalab.github.io/">Rafael Irizarry</a> of Dana Farber has online programs available through edX:
<ul>
<li><a href="https://www.edx.org/professional-certificate/harvardx-data-science">Introduction to Data Science</a></li>
<li><a href="https://www.edx.org/professional-certificate/harvardx-data-analysis-for-life-sciences">Data Analysis for Life Sciences</a></li>
<li><a href="https://www.edx.org/professional-certificate/harvardx-data-analysis-for-genomics">Data Analysis for Genomics</a></li>
</ul></li>
<li><em>Generally speaking, edX courses are all free to audit for a limited period of time. Unlimited access and the ability to earn a course Certificate will require payment</em></li>
</ul></li>
<li><a href="https://www.coursera.org">Coursera</a>: Offers a collection of courses for <a href="https://www.coursera.org/browse/data-science">Data Science</a> and <a href="https://www.coursera.org/browse/life-sciences/bioinformatics">Bioinformatics</a>
<ul>
<li><a href="https://www.coursera.org/specializations/data-science-foundations-r">R Programming</a>: A beginner-level program has five mini-courses. It takes about 4 months to complete.</li>
<li><a href="https://www.coursera.org/specializations/statistics">Statistics with R</a>: A beginner-level program with five mini-courses. It takes about 7 months to complete.</li>
<li><a href="https://www.coursera.org/specializations/genomic-data-science">Genomic Data Science</a>: An intermediate-level program for those who are already acquainted with R. It has eight mini-courses. It takes about 6 months to complete.</li>
<li><a href="https://www.coursera.org/specializations/data-science-python">Python Programming</a>: An intermediate-level program that takes about 4 months to complete.</li>
<li><em>Coursera offers a 7-day free trial, and is a paid subscription service after</em></li>
</ul></li>
<li><a href="https://www.udacity.com">Udacity</a>: Offers a collection of courses for <a href="https://www.udacity.com/courses/school-of-data-science">Data Science</a>
<ul>
<li><em>Udacity is a paid subscription service</em></li>
<li><a href="https://blog.udacity.com/2020/03/one-month-free-on-nanodegrees.html">Currently offering one month free for their Nanodegree programs.</a></li>
</ul></li>
<li><a href="https://www.udemy.com">Udemy</a>: Offers a collection of courses for <a href="https://www.udemy.com/courses/development/data-science/">Data Science</a>
<ul>
<li><em>Udemy offers courses at various price points.</em></li>
<li>Keep an eye out for sales which happen regularly and can drastically reduce the cost.</li>
</ul></li>
<li><a href="https://cognitiveclass.ai/">CognitiveClass.ai</a> Offers a collection of courses for data science, AI, and cloud computing.
<ul>
<li><em>All courses are free</em></li>
</ul></li>
<li><a href="http://datasciencemasters.org">The Open Source Data Science Masters</a>: An open-source curriculum for learning data science. This is a mixed media course made up of videos, books, and slides.
<ul>
<li><em>Some content is free, some is paid</em></li>
</ul></li>
<li><a href="http://work.caltech.edu/telecourse">CalTech</a> Learning from Data
<ul>
<li><em>A free YouTube series</em></li>
</ul></li>
<li><a href="https://www.dataquest.io/">DataQuest</a>: A subscription service that offers programs and courses focused on data analysis and engineering in Python and R.
<ul>
<li><em>Tiered payment system with basic and premium plans</em></li>
</ul></li>
<li><a href="https://www.codecademy.com/">CodeAcademy</a>: A subscription service that offers coding programs and courses in many different languages.
<ul>
<li><em>Tiered payment system with limited content available for free</em></li>
</ul></li>
</ul>
<p>* Completely overwhelmed? Don’t know where to start? <a href="https://forms.gle/8WkKbbpjg6AXTuMW7">Fill out this form</a> and let us know what’s going on.</p>
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