Bioinformatics@HSL: BBT Workshop Descriptions
Created by Health Science Librarians
UNC Bioinformatics Workshop Descriptions - New Spring 2025 Series
The Basic Bioinformatics Tools Workshop Series provides seminar and hands-on computer workshops on bioinformatics tools and resources to faculty, staff and students of UNC-Chapel Hill. This workshop series is sponsored by the UNC Health Sciences Library in partnership with the UNC Bioinformatics and Analytics Research Collaborative (BARC). Workshops are held at the Health Sciences Library in the HSL 329 classroom (3rd floor).
In Spring 2025 we launched a new series of workshops focusing on Single Cell RNA technologies and analysis methods. Below are descriptions of workshops that were offered this spring.
Introduction to Single Cell RNA (scRNA) Technologies and Analysis Methods: An 8-Workshop Series
The eight, one-hour Introduction to Single Cell RNA (scRNA) Technologies and Analysis Methods workshops below are a chained sequence of workshops to introduce participants to common single-cell based techniques and standard methods of handling and analyzing these data types. Each class will build upon the prior class and each session is a prerequisite for the next class in the eight-workshop series.
Account Requirement: To participate in these workshops, you will need an account on the “Longleaf” Linux cluster managed by ITS Research Computing. Follow instructions for requesting a “Longleaf” account on the ITS Research Computing website: https://help.rc.unc.edu/request-a-cluster-account/. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.
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1. Intro to OnDemand and R
Description: This session will cover how to connect to UNC OnDemand and start RStudio, as well as an introduction to programming in R and installing packages.
Time: Wednesday 2/19/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line.
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2. scRNA-seq Methods and Data Structures
Description: This session will provide a brief overview of scRNA-seq technologies (10x Genomics Chromium, Parse Biosciences, Complete Genomics Stereo-seq, and their data outputs. We will go over what some of these data look like and how they are organized.
Time: Wednesday 2/26/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R workshop above.
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3. Quality Control
Description: This session will cover best practices for assessing the quality of a scRNA dataset and methods for filtering potentially low-quality cells.
Time: Wednesday 3/5/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R and scRNA-seq Methods and Data Structures workshops above.
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4. Normalization and Sample Integration
Description: This session will provide a description of different normalization methods and how to perform them with Seurat. We will also introduce the idea of sample integration (i.e. batch correction) and how to perform some of the more common integration methods.
Time: Wednesday 3/19/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R, scRNA-seq Methods and Data Structures, and Quality Control workshops above.
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5. Dimensionality Reduction
Description: This session will cover what dimensionality reduction is, types of reductions (PCA, TSNE, UMAP), how to perform them in Seurat, and some ways to assess reductions.
Time: Wednesday 3/26/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R, scRNA-seq Methods and Data Structures, Quality Control, and Normalization and Sample Integration workshops above.
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6. Clustering
Description: In this session we will cover how to cluster data, different clustering methods, and some strategies for determining optimal parameters for clustering.
Time: Wednesday 4/2/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R, scRNA-seq Methods and Data Structures, Quality Control, Normalization and Sample Integration, and Dimensionality Reduction workshops above.
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7. Annotating Cell Types
Description: In this session we will cover how to identify cluster markers, annotate cell types with reference atlases, and annotate with other published single cell (sc) datasets.
Time: Wednesday 4/9/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R, scRNA-seq Methods and Data Structures, Quality Control, Normalization and Sample Integration, Dimensionality Reduction, and Clustering workshops above.
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8. Differential Analysis
Description: In this final class we will go through how to perform a pseudo-bulk differential gene expression analysis between different clusters/cell types identified in a single cell (sc) dataset.
Time: Wednesday 4/16/2025, 10:00am - 11:00am
Instructor: Matt Niederhuber, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329
Account Requirement: See Account Requirement above.
Prerequisites: Some programming experience and comfortable using command line. Intro to OnDemand and R, scRNA-seq Methods and Data Structures, Quality Control, Normalization and Sample Integration, Dimensionality Reduction, Clustering, and Annotating Cell Types workshops above.
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