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

L’université Harvard (Harvard University), ou plus simplement Harvard, est une université privée américaine située à Cambridge, ville de l'agglomération de Boston, dans le Massachusetts. Fondée le 28 octobre 1636, c'est le plus ancien établissement d'enseignement supérieur des États-Unis.
Elle fait partie de l'Ivy League, regroupement informel des huit universités de la côte Est des États-Unis. Plus de 70 de ses étudiants ont reçu un prix Nobel. Le corps enseignant est constitué de 2 497 professeurs, pour 6 715 étudiants de premier cycle (undergraduate, en anglais) et 12 424 étudiants de cycle supérieur (graduate en anglais). Harvard attire des étudiants du monde entier (132 nationalités représentées en 2004).
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