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Applied Bioinformatics

Welcome to the Applied Bioinformatics course offered at The Scripps Research Institute.

Instructors: Dr. Andrew I Su (@andrewsu)
Teaching Assistants (TAs):

This course is available in 2 parts and operates under the Computational Biology & Bioinformatics (CBB) core track:

  • Fundamentals of Scientific Computing, 4 weeks (1 credit)

    1. Learn how to use RStudio and R
    2. Learn basics of data visualization and exploratory data analysis
    3. Learn to use R Notebooks
  • Applied Bioinformatics and Computational Biology (ABCB), 8 weeks (2 credits)

    1. Learn the fundamentals of exploratory analysis of RNA-seq data, including PCA and clustering
    2. Learn the fundamentals of differential expression analysis, enrichment analysis, and visualization
    3. Practice and present on learned R skillset through published data via Capstone project.

Prerequisites

  • A recent computer running Windows 10/11, MacOS, or Linux (inform instructors if you have any concerns)
  • Software installation prior to first class (instructions)

Course Materials

This section will be updated as the course progresses.

  • Tuesday 2022-09-06: Course intro
    • slides
    • Homework due Monday 2022-09-12 3PM PT
  • Thursday 2022-09-08: Data visualization
    • slides
    • Homework due Monday 2022-09-19 3PM PT
  • Tuesday 2022-09-13:
    • slides
    • Homework due Monday 2022-09-19 3PM PT
  • Thursday 2022-09-15:
    • slides (to be posted)
    • Homework due Monday 2022-09-26 3PM PT

Credit to past instructors and TAs: Dr. Sabah Ul-Hasan (@sabahzero), Dr. Huitian Yolanda Diao (@Huitian), Dr. Karthik Gangavarapu (@gkarthik), Shang-Fu Chen (@ShaunFChen), Jerry Zak (@trebbiano)