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Hands-on Bioinformatics Workshops

Reproducible Research in R

Dates: Part 1 - Wednesday, May 25, Part 2 - Friday, May 27

Time: 11:00am-12:30pm

Location: Virtual

Target Audience

  • R users familiar with basic coding concepts:
    • Basic language syntax
    • Navigating file trees, relative / absolute paths
    • Using and defining functions
    • Writing analysis .R scripts

This workshop addresses reproducible research methods using R, highlighting project-oriented workflows and analytically reproducible documents (i.e., literate programming) with R Markdown and knitr. Additionally, attendees will be introduced to version control with Git. Principles of reproducibility are demonstrated using example data from the Gene Expression Omnibus. Attendees should be interested in applying custom scripts to their own analysis workflows. While this workshop is geared towards users with prior R experience, these principles are applicable to other languages and frameworks utilized for bioinformatics and computational biology. Life scientists can apply these skills to their own research domain, where an emphasis on robust development practices is encouraged.

Accessibility

This workshop will utilize the Interactive Data Analytics Service (IDAS) maintained by ITS Research Services. Attendees will be provided with access to a standardized RStudio environment, relevant R packages, and the necessary development tools for version control. This resource is available to current students, staff, and faculty with an active Hawk ID. IDAS offers a quite suitable environment for reproducible research, offering integration with campus HPC resources and shared drives.

Registration: This class size is limited to 15 and is restricted to University of Iowa faculty/staff/students. Email iihg-bioinformatics@uiowa.edu if you are interested in attending. If registration fills up, you will be placed on a waiting list and we will schedule another workshop for a later date.


Recordings

Visit our YouTube channel to view recordings of othe workshops and seminars we've hosted:


Previous events:

  • Visualization of RNA Sequencing Data with PCA clustering and Heatmaps in R/R Studio
    Thursday, November 18, 2021
    Henry Keen, PhD

  • Ingenuity Pathway Analysis Training: Dataset analysis and knowledge base queries using Qiagen IPA
    Wednesday, September 29 and Thursday, September 30, 2021