Bioinformatics workshops - Spring 2025
We continuously organize basic and advanced workshops on a wide range of bioinformatics topics. These workshops are designed to address practical issues often encountered in bioinformatics work. They are designed to help users understand and work with the CRCD clusters.
Free and open to everyone at University of Pittsburgh and its affiliates.
Participants must be physically present in order to participate. The conference room can accommodate ~30 attendees. Attendees are seated on a first-come, first-served basis. To ensure a high-quality experience for all participants and instructors, remote attendance is not accommodated.
Please note that you will need to bring your own laptop to connect to CRCD clusters. Access to CRCD clusters requires an account. If you do not yet have an account on CRCD clusters, we will create a temporary account for you. You will connect to Pitt wireless from your own laptop. You will logon ondemand.htc.crc.pitt.edu and run RStudio server, Jupyter Notebooks or submit batch jobs during the workshop. You do not need to install any software on your own laptop.
Some basic understanding of R or Python programming and the Linux environment will be advantageous, but is not required. All scripts will be carefully explained to allow all attendees understanding the rationale.
Register for all workshops: Register
10X single cell techniques and Getting started with Cellranger
Tuesday, Feb. 4, 1:00pm-4:00pm
The workshop will begin with a brief overview of the single cell resources offered by 10X Genomics and provided through the Single Cell Core. Products discussed will include 3’ and 5’ gene expression, fixed RNA profiling (FLEX) and multiome (ATAC + gene expression from the same cell).
This workshop will teach users on how to perform sample demultiplexing, barcode processing, single cell 3’ and 5’ gene counting V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data using 10x Genomics’ Cell Ranger analysis pipeline.
Prerequisite: CRC user account
Presented by Single cell core Heidi Monroe and Oge Ezenwa
Single cell data analysis using Seurat
Tuesday, Feb. 11, 1:00pm-4:00pm
This hands-on workshop introduces the analysis of single cell data using Seurat. The users will learn how to process Cell Ranger count matrices into a Seurat object, run standard pre-processing steps for scRNA-seq data in Seurat which involves selection and filtration of cells based on QC metrics, data normalization and scaling, and detection of highly variable features. We will also show how to identify cell types and answer biological questions using differential gene analysis.
Prerequisite: CRC user account, Beginner level R
Presented by Oge Ezenwa
Single-cell trajectory inference methods
Tuesday, Feb. 18, 1:00pm-4:00pm
Tuesday, March. 25, 1:00pm-4:00pm (rescheduled)
Single-cell trajectory inference is a computational technique to study cell development over time. In this workshop, we will theoretically introduce the concept of trajectory inference and pseudo-time. In the practical section, we will hand on a real single-cell dataset to run through the computational pipelines. Single-cell clustering, trajectory inference, pseudo-time calculation, visualization, and differential analysis will be introduced. Presented by Silvia Liu
RNA velocity of single cells
Tuesday, Feb. 25, 1:00pm-4:00pm
In this workshop, we will provide a comprehensive introduction to single-cell RNA velocity, a method used to infer the future transcriptional states of cells in dynamic biological processes by analyzing the spliced and unspliced mRNA. Participants will gain hands-on experience with real single-cell datasets using a Python package scVelo to 1). understanding the different analyzing modes for RNA velocity: deterministic, stochastic, and dynamical, 2). estimating RNA velocity, 3) identifying dynamic genes, and 4). visualization to explore cellular transitions. For incorporation of chromatin accessibility data, the python package MultiVelo will also be presented for examining the temporal relationship between the epigenome and transcriptome.
Prerequisite: CRC user account, beginner level Unix and Python
Presented by Jiefei Wang and Tracy Tabib
Single cell gene regulatory network analysis
Tuesday, March 11, 1:00pm-4:00pm
Jishnu Das
Co-expression inference from single cell sequencing data
Tuesday, March 18, 1:00pm-4:00pm
Dhivyaa Rajasundaram
Integrative single cell RNA-seq and ATAC-seq data analysis
Tuesday, April 1, 1:00pm-4:00pm
This hands-on workshop focuses on demonstrating how to analyze a single-cell dataset that captures both DNA accessibility and gene expression in the same cells. Using the Signac and Seurat packages, attendees will learn to:
- Annotate scATAC-seq datasets using an existing scRNA-seq dataset.
- Co-visualize cells from scRNA-seq and scATAC-seq experiments.
- Project scATAC-seq cells onto a UMAP derived from scRNA-seq data for integrative analysis.
This workshop emphasizes practical, hands-on experience for effective multiomic single-cell data interpretation.
Prerequisite: CRC user account, Beginner level R
Presented by Oge Ezenwa
Reference Mapping of single cell data
Tuesday, April 8, 1:00pm-4:00pm
Single-cell reference mapping aims to map a query dataset to a well-studied reference dataset. In this workshop, we will introduce how to perform dimension reduction, visualization and clustering using reference mapping strategies. In the first half, we will provide a theoretical introduction of these concepts. In the second half, we will hand on a query and a reference dataset to run through the pipelines. In addition to the in-house reference dataset, we will also introduce data mining on some public single-cell atlases. Presented by Silvia Liu
Single cell TCR data analysis
Tuesday, April 15, 1:00pm-4:00pm
Dhivyaa Rajasundaram
Bioinformatics workshops - Older versions
| Semester | Links |
|---|---|
| Fall 2024 | Bioinformatics workshop materials |
| Spring 2024 | Bioinformatics workshop materials |
| Fall 2023 | Bioinformatics workshop materials |
| Spring 2023 | Bioinformatics workshop materials |
| Fall 2022 | Bioinformatics workshop materials |
| Summer 2022 | Bioinformatics workshop materials |
| Spring 2022 | Bioinformatics workshop materials |
| Fall 2021 | Bioinformatics workshop materials |
| Summer 2021 | Bioinformatics workshop materials |
| Spring 2021 | Bioinformatics workshop materials |
| Fall 2020 | Bioinformatics workshop materials |