MolBio Classes and Customized Trainings

To request a class, please contact MolBio.

Bulk RNA-seq data analysis using CLC Genomics Workbench

Participants will learn how to access the CLC Genomics Server hosted on the HTC Cluster by Pitt CRC; import RNA-Seq FASTQ reads from a GEO dataset; assess the quality of RNA-Seq data; align reads to a reference genome; estimate known gene and transcript expression; perform differential expression analysis; and visualize data by generating PCA, volcano plot and heatmaps.

ChIP-Seq

This is a 4-hour workshop. The morning session (10am - 12pm) provides a brief introduction to techniques, platforms, and methods used in chromatin profiling experiments, including Transcription Factor / Histone ChIP-Seq and ATAC-Seq. The afternoon session (1pm - 3pm) focuses on hands-on data analysis practice using HSLS-licensed CLC Genomics Workbench, Partek Flow, and TRANSFAC/Match software.

CITE-Seq and Spatial Transcriptomics Data Analysis with Partek Flow

In this workshop, we will cover such multiomics data analysis - CITE Seq and Spatial Transcriptomics. Participants will learn how to import 10x Genomics CITE-Seq and Spatial Transcriptomics (Visium) data to PartekFlow; merge expression data with histological information; filter and normalize the data; and generate PCA, t-SNE, and UMAP plots to visualize data.

CLC Genomics Workbench Overview

This workshop would provide a brief overview of HSLS-licensed CLC Genomics Workbench, a comprehensive analysis package for genomics, transcriptomics, and epigenomics research.

Topics to be covered are:
• What’s new in version 23
• Super fast read mapping From fastq to VCF
• Bullk RNA-seq improvements
• Single-cell data analysis tools

Command Line for Biologists

This workshop will teach how to (1) access a remote Unix machine (Center for Research Computing- HTC Cluster) (2) use basic Unix commands for managing files and directories, and (3) transfer files using FTP client software (4) access HTC Cluster-installed open-source bioinformatics software packages.

Data Visualization in R using ggplot2

This hands-on workshop will cover the creation of data visualizations using the ggplot2 package in R. Upon completion, participants will be able to create various graphical summaries of data, describe the “grammar” of ggplot2 functions, and build custom visualizations with ggplot2.

Data Visualization in R with ggPlot2 - In-Person

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 view on your schedule. During the in-person hands-on session, you will learn how to solve the exercise problems.

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.

EHR and Survey Data Analysis

One of the biggest strengths of the All of Us dataset is data from surveys. This workshop will provide details about the survey data present in All of Us and show how to use that data within a project, including how to link the data to concept sets and EHR data datasets.

Exploring Microbial Genomics with CLC Genomics Workbench

The workshop will focus on microbial genomics data analysis with CLC Genomics Workbench. You will learn how to:
- Perform microbial genomics data analysis with ease and accuracy
- Conduct AVS (antiviral screening) analysis
- Perform hybrid viral sequencing
- Generate whole genome taxonomies profiles and AMR (antimicrobial resistance) reports

Exploring Microbial Genomics with CLC Genomics Workbench (online)

The workshop will focus on microbial genomics data analysis with CLC Genomics Workbench.

You will learn how to:
- Perform microbial genomics data analysis with ease and accuracy
- Conduct AVS (antiviral screening) analysis
- Perform hybrid viral sequencing
- Generate whole genome taxonomies profiles and AMR (antimicrobial resistance) reports

Gene Expression Data Mining and Analysis

This workshop will focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies - bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data, and generate a list of differentially expressed genes (DEG) between two conditions (disease state vs. normal, drug treatment vs. control, virus infection vs. mock treatment). We will use a variety of bioinformatics tools such as BioJupies, Correlation engine, GEO2R, etc. Additionally, best practices and guidelines on how to submit your own high throughput gene expression data to GEO will also be discussed.

Gene Expression Visualization using PartekFlow and Cytoscape

This workshop will cover gene expression visualization techniques using Partek flow and Cytoscape.

Gene Regulation

This workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to HSLS-licensed TRANSFAC/Match and Correlation Engine software and open-access tools such as the UCSC genome browser and Cistrome data browser.

Genetic Variation

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 - 3:00 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.

Genome Browsing

This hands-on workshop focuses on a variety of genome biology resources. Learn to (1) identify and retrieve whole genome sequence information by searching databases (NCBI Genome, Integrated Microbial Genome), (2) navigate genome sequences and extract information from annotated genome data (UCSC Genome Browser), (3) construct complex queries and retrieve large-scale genome data (Table Browser), and (4) create custom genome browser tracks from users’ own uploaded data (UCSC Custom Track tool).

Introduction to All of Us Researcher Workbench

The All of Us Research Program (AoURP), led by the National Institutes of Health, is a longitudinal cohort study aimed at advancing precision medicine and improving human health

Introduction to R

This is a flipped class; links to PowerPoint slides, lecture videos, and practice exercises that you can view on your schedule are available upon registration. During the session, you will learn how to solve the exercise problems.

Introduction to R and Data Wrangling - Online

This class will cover the basics of R programming for data analysis and graphics. This is a flipped class; links to PowerPoint slides, lecture videos, and practice exercises that you can view on your schedule are available upon registration. During the class, you will learn how to solve the exercise problems.

Overview of CLC Genomics Workbench (online)

This workshop would provide a brief overview of HSLS-licensed CLC Genomics Workbench, a comprehensive analysis package for genomics, transcriptomics, and epigenomics research.

Topics to be covered are:

•   What’s new in version 23
•   Super fast read mapping From fastq to VCF
•   Bulk RNA-seq improvements
•   Single-cell data analysis tools

Overview of molecular data repositories and GEO Data mining

This workshop will cover the Overview of NIH supported data repositories with specific focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies - bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data, and generate a list of differentially expressed genes (DEG) between two conditions. We will use a variety of bioinformatics tools such as R shiny app iDEP, Correlation engine, GEO2R, etc.

Pathway Enrichment Analysis using GSEA and g:Profiler

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.

Pathway Enrichment Analysis using IPA and CE

This workshop uses two library-licensed software - Ingenuity Pathway Analysis (IPA) and Illumina's Correlation Engine (CE) to teach biological pathway enrichment analysis. Upon registration, you will receive links to workshop materials (PowerPoint slides, lecture videos, and practice exercises) that you can view on your schedule. During the class, you will learn how to solve exercise problems.

Participants will learn how to:

Pathway Enrichment Analysis Using IPA and CE - In-Person

The workshop provides a brief overview of bioinformatics concepts and software used for interpreting a gene list using pathway and network information, followed by a step-by-step guide on pathway enrichment analysis using two HSLS-licensed tools: Correlation Engine, and Ingenuity Pathway Analysis (IPA)

Pathway Enrichment Analysis with IPA

This workshop provides a brief overview of bioinformatics concepts and software used for interpreting a gene list using pathway and network information and focuses on software demonstration and hands-on exercise using HSLS-licensed software: Ingenuity Pathway Analysis (IPA).

Programming in R

This workshop will cover the more advanced topics in R programming for data analysis and graphics. Upon completion participants will be able to import and export data, merge datasets, transform data, and create basic summaries of data.

RNA-Seq Data Analysis Using CLC Genomics Workbench - In-Person

This workshop briefly introduces techniques, platforms, and methods used in bulk RNA-Seq experiments, followed by a step-by-step guide for a bulk RNA-Seq data analysis using the HSLS licensed CLC Genomics Workbench software.

RNA-Seq Data Analysis using CLC Genomics Workbench - Online

scRNA-Seq Data Analysis using PartekFlow

This workshop introduces the techniques, platforms, and methods used in generating single-cell RNA-Seq data, followed by a software demonstration on data analysis using HSLS-licensed Partek Flow.

scRNA-Seq Data Analysis Using PartekFlow - In-Person

This workshop briefly introduces the techniques, platforms, and methods used in generating single-cell RNA-Seq data, followed by a step-by-step guide on scRNA-seq data analysis using HSLS-licensed Partek Flow software.

scRNA-Seq Data Analysis with CLC Genomics Workbench - Online

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

Terminology and Data Model Training

All of Us data includes data from electronic health records (EHR) for hundreds of thousands of people. This workshop will introduce the fundamentals of working with terminologies important to research using EHR data. The workshop will cover the construction of concept sets, important terminologies (ICD, SNOMED, LOINC, and RxNorm), and how to use them to subset patient data from the All of Us dataset.