• Length:
    4 Weeks
  • Effort:
    2–4 hours per week
  • Price:

    FREE
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  • Institution
  • Subject:
  • Level:
    Advanced
  • Language:
    English
  • Video Transcript:
    English
  • Course Type:
    Self-paced on your time

Associated Programs:

Prerequisites

About this course

Skip About this course

In this course, we begin with approaches to visualization of genome-scale data, and provide tools to build interactive graphical interfaces to speed discovery and interpretation. Using knitr and rmarkdown as basic authoring tools, the concept of reproducible research is developed, and the concept of an executable document is presented. In this framework reports are linked tightly to the underlying data and code, enhancing reproducibility and extensibility of completed analyses. We study out-of-memory approaches to the analysis of very large data resources, using relational databases or HDF5 as "back ends" with familiar R interfaces. Multiomic data integration is illustrated using a curated version of The Cancer Genome Atlas. Finally, we explore cloud-resident resources developed for the Encyclopedia of DNA Elements (the ENCODE project). These address transcription factor binding, ATAC-seq, and RNA-seq with CRISPR interference.

Given the diversity in educational background of our students we have divided the series into seven parts. You can take the entire series or individual courses that interest you. If you are a statistician you should consider skipping the first two or three courses, similarly, if you are biologists you should consider skipping some of the introductory biology lectures. Note that the statistics and programming aspects of the class ramp up in difficulty relatively quickly across the first three courses. By the third course will be teaching advanced statistical concepts such as hierarchical models and by the fourth advanced software engineering skills, such as parallel computing and reproducible research concepts.

These courses make up two Professional Certificates and are self-paced:

Data Analysis for Life Sciences:

Genomics Data Analysis:

This class was supported in part by NIH grant R25GM114818.

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What you'll learn

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  • Static and interactive visualization of genomic data
  • Reproducible analysis methods
  • Memory-sparing representations of genomic assays
  • Working with multiomic experiments in cancer
  • Targeted interrogation of cloud-scale genomic archives

Meet your instructors

Rafael Irizarry
Professor of Biostatistics
Harvard University
Michael Love
Assistant Professor, Departments of Biostatistics and Genetics
UNC Gillings School of Global Public Health

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Who can take this course?

Unfortunately, learners from one or more of the following countries or regions will not be able to register for this course: Iran, Cuba and the Crimea region of Ukraine. While edX has sought licenses from the U.S. Office of Foreign Assets Control (OFAC) to offer our courses to learners in these countries and regions, the licenses we have received are not broad enough to allow us to offer this course in all locations. EdX truly regrets that U.S. sanctions prevent us from offering all of our courses to everyone, no matter where they live.