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.
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.
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 GSEA and g: Profiler results in Cytoscape will also be covered.
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 through a user-friendly, point-and-click graphical user interface, so neither computer programming experience nor familiarity with the command-line interface is required.
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 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 software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command-line interface is required.
This workshop is on the visualization of gene expression data using HSLS-licensed Partek Flow software as well as open-access Cytoscape software
Target Audience:
Experimental biologists seeking to learn how to visualize the 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.
Workshop Objective:
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-licensed software CLC Genomics Workbench, how to use bioinformatics tools for functional analysis of mutations, and open-access web tools such as Ensembl Variant Effect Predictor and wANNOVAR.
Target Audience:
Experimental biologists seeking to identify genetic variations from Whole Exome or Whole Genome Sequencing data. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.
Workshop Requirements:
Workshop Guide:
Attribution:
Please include the following statement in the acknowledgments section for all publications, posters, and presentations: Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.
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.
Target Audience:
Experimental biologists interested in analyzing bulk RNA-Seq and/or ChIP-Seq data, whether generated through their own experiments or retrieved from repositories such as GEO, will find this workshop particularly useful. The software covered in the workshop features a user-friendly, point-and-click graphical user interface, eliminating the need for programming experience or familiarity with the command-line interface.