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Hands-on Bioinformatics Workshops

Hello! Thank you for your interest in attending a Hands-on Bioinformatics Workshop hosted by the Iowa Institute of Human Genetics. Coming up in December, we have two workshops that are completely unrelated to one another so please pay close attention to what you are registering for.

Quarto Markdown Projects for Scientific and Technical Reports

Date: Thursday, December 8

Time: 11:00am-12:30pm

Location: 321 EMRB - In person only

Summary:

Quarto is a next-generation system for authoring scientific and technical documents in R/RStudio. This open-source publishing tool expands the capabilities of R Markdown with consistent syntax for rendering a variety of output formats (html, pdf, doc) and project types (e.g., articles, websites and presentations). For practitioners of scientific computation interested in approaches to reproducible research, this project-oriented workshop provides tutorials for rendering Quarto markdown documents into projects and serves as an entry point for migrating from R Markdown.

Registration:

This class size is limited to 12 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.


Introduction to Ingenuity Pathway Analysis (IPA)

Date: Wednesday, December 14

Time: 8:30am - 4:00pm

Location: Information Commons East - Hardin Library for Health Sciences

Part 1: Exploring public data using IPA

We will focus on how to use IPA without your own data. We will build networks from scratch, simulate activity changes, and explore public datasets using Pattern Search and Land Explorer.

  • Network construction, Molecule Activity Predictor, and Pattern Search (9:00-10:30 am)
  • Browsing public disease and cancer studies in Land Explorer (10:40-noon)
  • Optional hands-on help

Part 2: Interpreting your data using IPA

We will focus on how to analyze your own data in IPA. We will upload a dataset, run a core analysis, learn how to interpret pathway and regulator results, and use Analysis Match to contextualize your data with the literature.

  • Upload, analysis settings, and interpreting your results (1:00-2:30 pm)
  • Compare your study with public results using Analysis Match (2:40-4:00 pm)
  • Optional hands-on help

Attendees are encouraged to follow along, and time will be set aside after each section to provide hands-on help. If anyone has any examples or research questions they’d like us to showcase, please email them to kyle.nilson@qiagen.com


Recordings

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


Previous events:

  • Reproducible Research in R
    Wednesday, May 25, 2022
    Jason Ratcliff, MS

  • 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