Bioinformatics Workshops

Kindly be aware that accessing the bioinformatics workshops materials located at the bottom of the page requires you to log in.

Bioinformatics workshops - Spring 2024

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 CRC clusters.

These workshops have hands-on components that require the following requirements be set up before a workshop begins.

  1. Participants should have an account on the HTC cluster, which is the cluster we will use for demonstration purposes. (page 1 of this documentation)
  2. This workshop also requires that participants either be on a Pitt network (hard-line) or behind a VPN. (page 2 of this documentation)
  3. You can submit jobs, i.e., your group's account has not expired, and your group's service units (CPU-hours) have not been exhausted entirely (page 4 of this documentation)

As a general rule, we offer no troubleshooting for technical setup issues at the workshops themselves! Therefore, be aware that if you do not set up the workshop's technical prerequisites well in advance, you may not be able to participate fully in its hands-on activities.

Please note: workshops will be presented in a hybrid format with up to 20 in-person participants. If you register for an in-person session and the in-person session is full, you will be alerted and receive a video conferencing link via the e-mail address you provide. CRC will continue to follow University guidelines regarding COVID-19 precautions, so other changes could be possible depending on those guidelines.

Register for all workshops: Spring 2024 bioinformatics workshops

The Single-Cell Spatial Transcriptomics Analysis (ScSTA) Cookbook
Tuesday, Feb. 20, 2024, 1:00pm - 4:00pm
This workshop aims to provide attendees with comprehensive knowledge and hands-on experience in the data analysis of sub-cellular resolution single-cell spatial transcriptomics (ScST) technologies such as Nanostring CosMx and 10X Genomics Xenium. We will start with an introduction to the components of ScST, including image registration, cell segmentation, cell type identification, spatial gene expression analysis, and more. A hands-on guided tutorial using real-world lung adenocarcinoma and COVID-19 datasets will follow. Presented by Arun Das

Protein interactome networks and gene regulatory networks in systems immunology

Tuesday, March 5, 2024, 1:00pm - 4:00pm
The workshop will provide a high-level overview of how protein-protein interaction networks and gene regulatory networks can be used in systems immunology research. Fundamental concepts as well as context-specific applications will be covered. This interactive workshop will include hands-on demos. Presented by Jishnu Das

An Introduction to Nvidia Parabricks
Tuesday, March 19, 2024, 1:00pm - 4:00pm
I will review accelerated computing for genomics. Illumina DRAGEN is FPGAs-accelerated, while  NVIDIA Clara Parabricks is a GPU-accelerated computational genomics application framework. I will provide an overview of NVIDIA’s Clara Parabricks software for accelerated secondary analysis in genomics including deep-learning-based tools. I will highlight the features of the latest version and demo how to use the free version of it on CRC's GPU cluster. Presented by Fangping Mu

Long-read sequencing

Tuesday, March 26, 2024, 1:00 pm - 4:00pm
This workshop will provide a quick glance of the long-read/ third-generation sequencing technology. In the first half, theoretical introduction of the long-read technology, platforms and diverse applications will be provided. In the second half, a hand-one practice on long-read RNA-seq data analysis will be performed, including quality control, alignment, gene/isoform quantification and fusion detection. Presented by Silvia Liu

Introduction to R with tidyverse
Tuesday, April 2, 2024, 1:00pm - 4:00pm
This workshop, designed for novice R users, will teach the basic concepts of using the tidyverse suite of packages in R for data science. Users will get hands-on practice in three domains: 1) R basics, 2) data wrangling, and 3) data visualization. Presented by Jenna Carlson

R shiny programming
Tuesday, April 16, 2024, 1:00pm - 4:00pm
This workshop will explore the principles behind creating user-friendly R Shiny apps tailored for various biomedical applications. We will also introduce strategies for enhancing the functionality and interactivity of R Shiny apps by integrating other programming languages like HTML, JavaScript, and Python. Attendees will have hands-on experience with various R Shiny layouts. Presented by Yu-Chiao Chiu