About the content
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:
- PH525.1x: Statistics and R for the Life Sciences
- PH525.2x: Introduction to Linear Models and Matrix Algebra
- PH525.3x: Statistical Inference and Modeling for High-throughput Experiments
- PH525.4x: High-Dimensional Data Analysis
Genomics Data Analysis:
- PH525.5x: Introduction to Bioconductor
- PH525.6x: Case Studies in Functional Genomics
- PH525.7x: Advanced Bioconductor
This class was supported in part by NIH grant R25GM114818.
HarvardX requires individuals who enroll in its courses on edX to abide by the terms of the edX honor code. HarvardX will take appropriate corrective action in response to violations of the edX honor code, which may include dismissal from the HarvardX course; revocation of any certificates received for the HarvardX course; or other remedies as circumstances warrant. No refunds will be issued in the case of corrective action for such violations. Enrollees who are taking HarvardX courses as part of another program will also be governed by the academic policies of those programs.
HarvardX pursues the science of learning. By registering as an online learner in an HX course, you will also participate in research about learning. Read our research statement to learn more.
Harvard University and HarvardX are committed to maintaining a safe and healthy educational and work environment in which no member of the community is excluded from participation in, denied the benefits of, or subjected to discrimination or harassment in our program. All members of the HarvardX community are expected to abide by Harvard policies on nondiscrimination, including sexual harassment, and the edX Terms of Service. If you have any questions or concerns, please contact firstname.lastname@example.org and/or report your experience through the edX contact form.
- 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
Professor of Biostatistics
Assistant Professor, Departments of Biostatistics and Genetics
UNC Gillings School of Global Public Health
Harvard University is a private Ivy League research university in Cambridge, Massachusetts. Established in 1636 and named for its first benefactor clergyman John Harvard, Harvard is the United States' oldest institution of higher learning, and its history, influence, and wealth have made it one of the world's most prestigious universities. The Harvard Corporation is its first chartered corporation. Although never formally affiliated with any denomination, the early College primarily trained Congregational and Unitarian clergy. Its curriculum and student body were gradually secularized during the 18th century, and by the 19th century, Harvard had emerged as the central cultural establishment among Boston elites. Following the American Civil War, President Charles W. Eliot's long tenure (1869–1909) transformed the college and affiliated professional schools into a modern research university; Harvard was a founding member of the Association of American Universities in 1900. A. Lawrence Lowell, who followed Eliot, further reformed the undergraduate curriculum and undertook aggressive expansion of Harvard's land holdings and physical plant. James Bryant Conant led the university through the Great Depression and World War II and began to reform the curriculum and liberalize admissions after the war. The undergraduate college became coeducational after its 1977 merger with Radcliffe College.
The university is organized into eleven separate academic units—ten faculties and the Radcliffe Institute for Advanced Study—with campuses throughout the Boston metropolitan area: its 209-acre (85 ha) main campus is centered on Harvard Yard in Cambridge, approximately 3 miles (5 km) northwest of Boston; the business school and athletics facilities, including Harvard Stadium, are located across the Charles River in the Allston neighborhood of Boston and the medical, dental, and public health schools are in the Longwood Medical Area. The endowment of Harvard's is worth $37.1 billion, making it the largest of any academic institution.
Harvard is a large, highly residential research university. The nominal cost of attendance is high, but the university's large endowment allows it to offer generous financial aid packages. The Harvard Library is the world's largest academic and private library system, comprising 79 individual libraries holding over 18 million items. The University is cited as one of the world's top tertiary institutions by various organizations.
Harvard's alumni include eight U.S. presidents, several foreign heads of state, 62 living billionaires, 359 Rhodes Scholars, and 242 Marshall Scholars. To date, some 157 Nobel laureates, 18 Fields Medalists, and 14 Turing Award winners have been affiliated as students, faculty, or staff. In addition, Harvard students and alumni have won 10 Academy Awards, 48 Pulitzer Prizes, and 108 Olympic medals (46 gold, 41 silver and 21 bronze).
Harvard University, the Massachusetts Institute of Technology, and the University of California, Berkeley, are just some of the schools that you have at your fingertips with EdX. Through massive open online courses (MOOCs) from the world's best universities, you can develop your knowledge in literature, math, history, food and nutrition, and more. These online classes are taught by highly-regarded experts in the field. If you take a class on computer science through Harvard, you may be taught by David J. Malan, a senior lecturer on computer science at Harvard University for the School of Engineering and Applied Sciences. But there's not just one professor - you have access to the entire teaching staff, allowing you to receive feedback on assignments straight from the experts. Pursue a Verified Certificate to document your achievements and use your coursework for job and school applications, promotions, and more. EdX also works with top universities to conduct research, allowing them to learn more about learning. Using their findings, edX is able to provide students with the best and most effective courses, constantly enhancing the student experience.