Books, educational resources, and teaching

Books

Genomics

Orchestrating Single-Cell Analysis in Bioconductor (OSCA). Online book that teaches users how to make use of cutting-edge Bioconductor tools to process, analyze, visualize, and explore single-cell RNA-seq data (scRNA-seq) data. Online companion for a manuscript published in Nature Methods.
- Authors: Robert Amezquita, Aaron Lun, Stephanie C. Hicks, Raphael Gottardo
Orchestrating Spatially-Resolved Transcriptomics Analysis with Bioconductor (OSTA). Online book that teaches users a computational analysis pipeline for spatially-resolved transcriptomics data.

Data Science

Tidyverse Skills for Data Science [Available on Leanpub] [Available via bookdown]. Online book that teaches users a powerful set of R packages known as the Tidyverse to learn the different aspects of the data science pipeline, from importing the data, tidying the data into a format that is easy to work with, exploring and visualizing the data, and fitting machine learning models. Online companion for the Tidyverse Skills for Data Science in R Specialization on Coursera.
- Authors: Shannon E. Ellis, Carrie Wright, Roger D. Peng and Stephanie C. Hicks

Massive Open Online Courses

Tidyverse Skills for Data Science in R Specialization

This five course massive open online course (MOOC) specialization series on Coursera allows learners to develop insights from data with tidy tools, such as data import, wrangle, visualize, and modeling data with the Tidyverse R packages. Instructors: Shannon E. Ellis, Carrie Wright, Roger D. Peng and Stephanie C. Hicks.

Coursera specialization: https://www.coursera.org/specializations/tidyverse-data-science-r

Open Case Studies

Individual case studies

The Open Case Studies (OCS) community resource of case studies that educators can use in the classroom to teach students how to effectively derive knowledge from data.

Educator’s guide to OCS

We have written an online book to help guide educators on how to most effectively use the Open Case Studies (either in or outside of the classroom), various entry points to using the case studies (including an R package to enable modular use of the case studies), how to modify and adapt components of the case studies for the classroom, and how to contribute new case studies. [Available as an online book]

Teaching experience

Cold Spring Harbor Laboratories (CSHL)

2023 | Co-Instructor, Computational Genomics (Teaching materials).
2022 | Co-Instructor, Computational Genomics (Teaching materials).
2022 | Co-Instructor, Statistical Analysis for Genome Scale Data (Teaching materials).
2015 | Teaching Assistant, Statistical Methods for Functional Genomics.

Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering

2024 | Co-Instructor, Computational Genomics: Data Analysis (EN.580.448)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health

2024 | Instructor, Statistical Programming Paradigms and Workflows (PH.140.777)
2023 | Instructor, Statistical Programming Paradigms and Workflows (PH.140.777)
2022 | Instructor, Statistical Programming Paradigms and Workflows (PH.140.840)
2022 | Instructor, Statistical Computing (PH.140.776)
2021 | Co-instructor, Advanced Data Science II (PH.140.712)
2021 | Instructor, Statistical Computing (PH.140.776)
2019 | Co-instructor, Advanced Data Science I and II (PH.140.711, PH.140.712)
2018 | Co-instructor, Advanced Data Science I and II (PH.140.711, PH.140.712)

Department of Data Sciences, Dana-Farber Cancer Institute

Department of Biostatistics, Harvard T.H. Chan School of Public Health

2016 | Co-instructor, Introduction to Data Science (HSPH - BIO 260).
2015 | Contributor and Discussion Leader, Harvard edX
- 1. Statistics and R for the Life Sciences (PH525.1x)
- 1. Case study: DNA methylation data analysis (PH525.8x)
2014 | Lead Teaching Fellow, Data Science (CS109), Harvard University. Supervised and guided 25 teaching fellows with over 300 students in the course. All course material available on* github.
2014 | Discussion Leader, Data Analysis for Genomics (PH525x), Harvard edX.

Department of Statistics, Rice University

2010, 2011 | Lead Teaching Assistant, Probability in Bioinformatics and Genetics (STAT 423, 623).
2010 | Lead Teaching Assistant, Applied Stochastic Processes (STAT 552).
2008, 2009 | Lab Instructor, Introduction to Statistics for the Biosciences (STAT 305).
2007, 2008 | Teaching Assistant, Probability and Statistics (STAT 310).

Louisiana State University

2005 - 2007 | Undergraduate tutor, tutored college algebra, trigonometry and pre-calculus students in the Roadmap 2 Redesign Program
2003 - 2004 | Undergraduate tutor, tutored students at Scotlandville Magnet High School in algebra