Class Type: Molecular Biology

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Pathway Enrichment Analysis & Visualization w/ Open Access Tools

The workshop is dedicated to exploring the intricate biology concealed within lists of differentially expressed genes. Participants will delve into an array of publicly accessible pathway enrichment analysis resources, such as the Gene Ontology (GO), Molecular Signature Database (MsigDB), Reactome, KEGG, and WikiPathways. Utilizing tools like GSEA and g:Profiler, the session will guide attendees in mining these databases effectively. Additionally, the workshop will provide comprehensive instruction on creating enrichment maps from GSEA and g:Profiler results using Cytoscape, thereby enhancing the participants' ability to visualize and interpret complex biological data.

All of Us Genomics Workshop: Investigating the Potential Impact of PCSK9 Variant on LDL Levels

Join us for our first-ever All of Us genomics workshop. In this workshop, we will focus on the PCSK9 gene and its connection to LDL levels for participants in the All of Us database. 

Using Electronic Health Record (EHR) data and provided genomic information, we will showcase a comprehensive approach that encompasses data cleaning and filtering to isolate specific genomic regions of interest. In addition to these preparatory steps, we will conduct a logistic regression analysis, utilizing disease status as the outcome variable and a single genetic variant as the predictor. These analytical skills serve as a solid foundation for future genome-wide association studies (GWAS) and provide a crucial resource for researchers. 

Target Audience: Researchers interested in the application of statistical methods to biological, genetic, and health-related data. 

Integrating ChIP-Seq/ATAC-Seq and Gene Expression Data: A Comprehensive Analysis using Partek Flow

This workshop is on integrated analysis of ChipSeq/ATAC Seq with gene expression data using HSLS-licensed Partek Flow software  

Target Audience: 

Experimental biologists seeking to learn how to analyze epigenomic or gene expression data generated through experiments or retrieved from a publication or a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither computer programming experience nor familiarity with the command-line interface is required.

CLC Genomics Workbench for Microbial Genomics Research

This class will provide an introduction to the use of CLC Genomics Workbench for microbial genomics analysis. Participants will learn how to access the CLCbio Genomics Server hosted by Pitt CRC, and will be introduced to the workflows and databases available in CLCbio. The workshop will cover amplicon-based analysis, including quality control (QC), OTU clustering and abundance, alpha and beta diversities, taxonomic analysis, and functional and drug resistance analysis.

Single cell Multiomics Analysis with Partek Flow 

Join us for an interactive workshop focused on single cell multiomics data analysis techniques covering CITE-Seq (gene + protein) and Multiome ATAC + Gene expression. You will gain practical experience using the Partek Flow software.

All of Us Researcher Workbench - EHR and Survey Data Analysis

In this workshop, you will learn how to create a project using concept sets, datasets, and workbooks, and discover how to use code snippets to accomplish more advanced tasks. You'll explore the full potential of the All of Us Researcher Workbench, gain practical skills in creating a project from start to finish, and learn how to use code snippets to enhance your research capabilities. Whether you're a new user of the All of Us Researcher Workbench or an experienced one, this workshop will provide valuable insights into leveraging the platform to meet your research needs.

All of Us Researcher Workbench - Terminology and Data Models Training

In this workshop, we will introduce the notion of concept sets and their role in observational research with Electronic Health Record (EHR) data. Whether you're a new user of the All of Us Researcher Workbench or an experienced one, this workshop will provide valuable insights into leveraging the platform to meet your research needs.

Agenda:

  • Introductory materials
  • Preliminary test of access
  • Health research use case of interest
  • Getting the featured workspaces working in your environment
  • The basic workflow for cohort and dataset creation
  • What happens next - "the usability cliff!"
  • Understanding the data model that holds AoU data
  • Workbooks to help you learn
  • A tour of the common data model, vocabulary, and workflow
  • Saving artifacts and reloading them

Introduction to All of Us Researcher Workbench

Join us for a class on the All of Us Researchers Workbench - a cloud-based platform that provides researchers with access to data generated by the All of Us Research Program (AoURP). Led by the National Institutes of Health, AoURP is a longitudinal cohort study to advance precision medicine and improve human health by partnering with one million or more diverse participants across the United States. Whether you're new to the platform or an experienced user, this class will provide valuable insights into leveraging the All of Us Researcher Workbench for your research needs.

Data Wrangling in R

This is a flipped class covering the more advanced topics in R programming for data analysis and the second part of a three-part series: Introduction to R; Data Wrangling in R, and Data Visualization in R. Upon registration, you will receive links to workshop materials (PowerPoint slides, lecture videos, and practice exercises) that you can view on your own schedule. During the hands-on in-person session, you will learn how to solve the exercise problems. 

If you need a refresher, please complete the lessons covered in the first part available via the workshop guide