Course Description

Foundations for Practical Single Cell RNA-seq Analyses will explore the use and analyses of single cell RNA-seq datasets that will enable precision exploration of the basic unit of life: the cell. This course will examine how single cell RNA-seq experiments are conducted, dive into the computational challenges and solutions to analyze these data, and extract biological meaning from the wealth of information afforded by single cell RNA-seq. It seeks to provide foundational concepts and bioinformatic skills to inquire about the wealth of information (and limitations) of single cell RNA-seq data. In addition to the didactic learning opportunities in the class, there will be practicum lectures and longitudinal project that will provide a hands-on analysis of a published, publicly available single cell dataset. These hands-on analyses will take learners through the computational techniques commonly employed in single cell RNA-seq data analyses.
At the end of the course, you will be able to assess and perform the foundational analyses for a standard single cell RNA-seq dataset using R. You will communicate your findings to peers and evaluate findings of published and peer analyses of single cell RNA-seq data.

Learner Outcomes

When you complete the course successfully, you will be able to:
  • Describe the advantages and limitations of various single cell RNA-seq approaches
  • Compare the quality and biases of different single cell RNA-seq datasets generated from the same tissues
  • Apply the best practices of single cell RNA-seq analyses to a set of published single cell RNA-seq datasets
  • Formulate and conduct an analysis plan to investigate specific hypotheses using single cell RNA-seq data
  • Draw biologically meaningful conclusions supported by data and analyses of single cell RNA-seq data


This course applies toward the Bioinformatics Endeavor digital badge.

Textbook Information

There is no textbook for purchase required for this course.


Statistics requires completion of one of the following:


R-Programming requires completion of one of the following:


Biological sciences requires completion of one of the following:

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