MolBio Classes and Customized Trainings

In this workshop, we will focus on the PCSK9 gene and its connection to LDL levels for participants in the All of Us database.

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 t...

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.

This workshop teaches bulk RNA-Seq data analysis using CLC Genomics Workbench software. Upon registration, you will receive links to workshop materials that you can view on your schedule. Target Audience Experimental biologists seeking to analyze bulk RNA-Seq data generated through experiments or retrieved from a repository such as GEO. The softwa...

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),...

This workshop aims to empower researchers with the essential skills needed to utilize bioinformatics tools operated through the Command Line Interface. It will cover Unix/Linux shell navigation, FTP transfers, file, and directory management, text editor functions, shell scripting, and data analysis with bioinformatics software.

This class covers the creation of data visualizations using the ggplot2 package in R. This is a flipped class and the third part of a 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 vi...

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...

This workshop is on the visualization of gene expression data using HSLS-licensed Partek Flow software as well as open-access Cytoscape software

This workshop provides an overview of resources and search strategies for transcriptional regulation. Emphasis will be placed on HSLS-licensed TRANSFAC/Match and Correlation Engine software, as well as open-access tools like the UCSC Genome Browser and the Cistrome Data Browser.

This is a 4 hour workshop. The morning session (10 am - 12 pm) provides a brief overview of human genetic variations with the introduction to various genetic variation databases (dbSNP, ClinVar, HGMD, COSMIC, TumorPortal, gnomAD, and RegulomeDb). The afternoon session (1 pm - 3 pm) covers variant identification using the HSLS-l...

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 ...

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...

This workshop adopts a flipped classroom model, providing you with access to PowerPoint slides, lecture videos, and practice exercises in the workshop guide for self-paced learning. During the class, you will have the opportunity to solve exercise problems with guidance from the instructor. This is the first part of a three-part series: Introductio...

In this engaging workshop, you will learn how to analyze differentially expressed genes (DEG) associated with genome-scale experiments, such as RNA-Seq gene expression studies, and gain mechanistic insights using Ingenuity Pathway Analysis and Correlation Engine software.

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...

This workshop focuses on uncovering the biology hidden behind the extracted differentially expressed gene list by searching publicly available pathway enrichment analysis resources, including Gene Ontology (GO), Molecular Signature Database (MsigDB), Reactome, KEGG, and WikiPathways using GSEA and g: Profiler. How to generate enrichment maps from G...

This is part 1 of a four-part Python Bootcamp. Day 1: In "Introduction to Python, Anaconda Navigator, and Jupyter Notebook," you'll familiarize yourself with the Anaconda Navigator interface and learn to create integrated Jupyter notebooks.

This is part 2 of a four-part Python Bootcamp. Day 2: "Data Centric Python with pandas" delves into Python's diverse data structures and unveils the analytical might of the pandas library, enhancing your data analysis skills.

This is part 3 of a four-part Python Bootcamp. Day 3: Advance your skills in "Data Exploration with pandas and Seaborn," focusing on data summarization and the art of visualization with Seaborn.

This is part 4 of a four-part Python Bootcamp. Description: Join us for our premiere Python Bootcamp Week, offering a comprehensive dive into Python programming. Mirroring the approach of its R counterpart, the bootcamp unfolds through a sequence of dedicated sessions that encompass the full data analysis workflow. This includes importing and clean...

This is part 1 of a four-part R Bootcamp. Description: Participate in our very first R Bootcamp Week for a deep dive into R programming. The bootcamp unfolds through a series of focused sessions that cover the entire data analysis process, from importing and cleaning data to sophisticated data manipulation and visualization techniques using the tid...

This is part 2 of a four-part R Bootcamp. Description: Participate in our very first R Bootcamp Week for a deep dive into R programming. The bootcamp unfolds through a series of focused sessions that cover the entire data analysis process, from importing and cleaning data to sophisticated data manipulation and visualization techniques using the tid...

This is part 3 of a four-part R Bootcamp. Description: Participate in our very first R Bootcamp Week for a deep dive into R programming. The bootcamp unfolds through a series of focused sessions that cover the entire data analysis process, from importing and cleaning data to sophisticated data manipulation and visualization techniques using the tid...

This is part 4 of a four-part R Bootcamp. Description: Participate in our very first R Bootcamp Week for a deep dive into R programming. The bootcamp unfolds through a series of focused sessions that cover the entire data analysis process, from importing and cleaning data to sophisticated data manipulation and visualization techniques using the tid...

This workshop will teach how to analyze, annotate and identify cell types in single-cell NGS data using the HSLS licensed CLC Genomics Workbench.

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.

This workshop is on single cell RNASeq analysis with multiple samples using HSLS-licensed Partek Flow software. Target Audience: Experimental biologists seeking to learn how to analyze the single cell data generated through experiments or retrieved from a publication or a repository such as GEO. The software covered in the workshop operates throug...

In this workshop, we will cover multiomics data analysis - CITE Seq and Spatial Transcriptomics. Participants are encouraged to work on solving the exercise problems during the hands-on session of the workshop.

A workshop designed to equip participants with essential skills in locating and analyzing gene expression studies using the Gene Expression Omnibus (GEO) repository.