UPCOMING SEMINAR:
REGISTER HERE: https://events.uchicago.edu/event/266381-cri-bioinformatics-workshop-series-10x-spatial
Bioinformatics Workshop Series: 10X Spatial Transcriptomics
Friday, May 22nd | 11:00am – 1:00pm CST.
Biological Sciences Learning Center (BSLC) Room #202 & via Zoom
Speaker: Jason Shapiro, PhD
The Center for Research Informatics invites you to an upcoming bioinformatics workshop. This workshop will introduce the audience to data analysis for 10X Spatial Transcriptomics technologies, including Visium, Visium HD, and Xenium. Topics for Visium analysis will include quality control, spatial clustering, deconvolution, cell-cell communication, and differential expression, with a discussion of how analyses change when working with Visium HD. The session will also cover the basics of Xenium analysis, including how to export and import data with the Xenium Explorer from 10X.
Topics Covered:
- Introduction to 10X Genomics Spatial Transcriptomics technologies
- Data preparation, quality control, and common pitfalls
- Spatially variable gene detection and clustering
- Deconvolution
- Differential Expression
- Cell-cell communication
This will be a 2 hour workshop, including time for questions.
This seminar will take place at Donnelley (BSLC) Meeting Room #202. 924 E 57th, Chicago, IL. also, via Zoom. Registration is required for all attendees, whether you plan to attend in person or via Zoom. Please note that due to limited capacity, registration may close early if capacity is reached. Participation is open to University of Chicago, UCM, and Pritzker School of Medicine faculty, staff, and students.
About the speaker: Jason, CRI Bioinformatician, received his PhD in Ecology and Evolutionary Biology from Yale University (2014). Prior to joining the CRI Bioinformatics Core in 2021, he was a postdoctoral research associate at Loyola University Chicago, where he developed computational methods to explore the diversity and evolution of bacteriophages. His research currently focuses on virus comparative genomics. Jason has experience working with a range of data types and bioinformatic questions, including microbiome analysis, genome assembly, network analysis, variant analysis, and transcriptomics, including single-cell and spatial datasets.
About the series: Since 2012, the Center for Research Informatics has offered free training sessions for the University of Chicago community in informatics research tools and techniques. Topics include REDCap, clinical data, bioinformatics analysis, data visualization, high performance computing, grant preparation, and more. To hear about upcoming seminars, sign up for our email list at https://cri.uchicago.edu/seminar-series.
Feedback Survey: We value your feedback and would appreciate if you would take a moment to complete our quick survey. Your insights will help us enhance our seminars and ensure they provide the best possible learning experience. Additionally, we welcome your suggestions for future seminar topics and any areas you’re interested in exploring further.
Questions? Contact Janaya Lee at janayalee@bsd.uchicago.edu.
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PAST SEMINARS
We archive our past training seminars here, including links to the content if it is available.
| Date | Topic | Seminar Title | Content |
|---|---|---|---|
| May 2026 | Bioinformatics | 10X Spatial Transcriptomics | COMING SOON |
| April 2026 | Bioinformatics | Bruker Spatial Transcriptomics: GeoMx and CosMx | Bruker Spatial Transcriptomics: GeoMx and CosMx Slides Recording of Bruker Spatial Transcriptomics: GeoMx and CosMx |
| March 2026 | Bioinformatics | AI-Assisted scRNA-seq Analysis Explorations, Use Cases and Pitfalls | AI-Assisted scRNA-seq Analysis Explorations, Use Cases and Pitfalls |
| January 2026 | AI & Data Science | Enhancing Clinical Data Science: Machine Learning and Advanced Techniques for Novel Insights in Clinical Research | Enhancing Clinical Data Science: Machine Learning and Advanced Techniques for Novel Insights in Clinical Research |
| November 2025 | Bioinformatics | Functional Enrichment Analysis | Functional Enrichment Data Analysis |
| October 2025 | Bioinformatics | Practical Workshop on Bulk RNA-seq Bioinformatics Pipelines | Bulk-RNAseq Pipeline Hands-on Training |
| June 2025 | Bioinformatics | scRNA-seq Data Integration | |
| April 2025 | Bioinformatics | Spatial Transcriptome Analysis | Spatial Transcriptomics Workshop |
| February 2025 | Bioinformatics | Bulk-RNAseq Pipeline | Bulk-RNAseq Pipeline Hands-on Training |
| October 2024 | CRI/BSDIS | Overview of CRI and BSDIS | CRI/BSDIS IT Expo Session |
| August 2024 | Bioinformatics | Using R Bioconductor packages for bulk RNA-seq DE analysis | Using R Bioconductor packages for bulk RNA-seq DE analysis |
| January 2024 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | |
| November 2023 | Data Analytics | Showcase of Reseach Project: NLP to Identify Mental Illness and Substance Use Factors in Clinical Notes | Case Illustration of NLP in a Research Project |
| November 2023 | Bioinformatics | Workshop Series: Part One Introduction to 10x Genomics Sequencing Protocols | Single Cell RNA-seq Data Analysis |
| February 2023 | REDCap | Introduction to REDCap | Introduction to REDCap |
| January 2021 | Data Analytics | Case Illustrations of NLP in Clinical Research | |
| May 2020 | HPC | Introduction to NVIDIA Parabricks | |
| April 2020 | REDCap | Making the Most of REDCap: All About Surveys | All About REDCap Surveys |
| February 2020 | REDCap | Making the Most of REDCap: Beyond the Basics | REDCap Beyond the Basics |
| January 2020 | HPC | Overview of CRI Computing Infrastructure | Overview of CRI Computing Infrastructure |
| May 2019 | Bioinformatics | Advanced Interactive Data Visualizations with Python | |
| March 2019 | Data Analytics | Using Natural Language Processing in Clinical Data Analytics | Using NLP in Clinical Data Analytics |
| February 2019 | Bioinformatics | Introduction to Reproducible Research via R Markdown | |
| December 2018 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| November 2018 | Clinical Data | Using the CRDW and Cohort Discovery Tools | CRDW and Cohort Discovery |
| October 2018 | Guest Talk | Introduction to the Human Imaging Research Office | Introduction to HIRO |
| September 2018 | HPC | Parallel Computing 101 | Parallel Computing 101 |
| August 2018 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| May 2018 | Clinical Data | Using the CRDW and Cohort Discovery Tools | CRDW and Cohort Discovery |
| April 2018 | HPC | CRI Infrastructure and New Parallel Storage | CRI Infrastructure and New Storage |
| March 2018 | Bioinformatics | Introduction to IPython and Pandas for Bioinformatics | iPython and Pandas |
| February 2018 | Clinical Data | Statistical Modeling with Clinical Data | Statistical Modeling - Methods Statistical Modeling - CRDW |
| December 2017 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| November 2017 | HPC | Computing with the CRI: Storage, HPC, and Virtual Servers | Computing with the CRI |
| October 2017 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | Biological Interpretation with IPA |
| September 2017 | Data Analytics | Using NLP in Clinical Data Analytics | NLP in Clinical Research |
| August 2017 | Grant Preparation | Including Informatics in Grant Applications | Informatics in Grants, Part 1 Informatics in Grants, Part 2 |
| May 2017 | Bioinformatics | Genomics Data Visualization | Genomics Data Visualization |
| April 2017 | HPC | HPC Workshop: Advanced | HPC: Advanced |
| April 2017 | HPC | HPC Workshop: Beginner | HPC: Beginner |
| November 2016 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | -- |
| November 2016 | Clinical Data | Optimizing Data Requests for the CRDW | Optimizing CRDW Requests |
| October 2016 | HPC | Introduction to Gardner: The CRI's New HPC Cluster | Introduction to Gardner |
| April 2016 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | -- |
| December 2015 | Bioinformatics | Annual Workshop: Bioinformatics Analysis of Integrative -Omics Data | Workshop Recap |
| October 2015 | Bioinformatics | Introductory Statistics with R | Introductory Statistics with R |
| September 2015 | Bioinformatics | Introduction to iPython and Pandas, Part II | iPython and Pandas, Part II |
| June and July 2015 | Bioinformatics | Introduction to iPython and Pandas, Part I | iPython and Pandas, Part I |
| May 2015 | Bioinformatics | Introduction to Python Programming, Part II | Introduction to Python, Part II |
| April 2015 | Bioinformatics | Introduction to Python Programming, Part I | Introduction to Python, Part I |
| March 2015 | Bioinformatics | Analysis of Affymetrix Microarray Data with R and Bioconductor | Analysis of Affymetrix Microarray Data |
| February 2015 | Bioinformatics, HPC | Introduction to CRI’s HPC Cluster for Bioinformatics Computing | Introduction to CRI's HPC Cluster |
| January 2015 | Bioinformatics | R Graphics for Bioinformatics | R Graphics for Bioinformatics |
| December 2014 | Bioinformatics | Annual Workshop: Bioinformatics Analysis of High-Throughput Genomics Data | Workshop Recap |
| October 2014 | Bioinformatics | Visual Exploration of Data with the Advanced R Graphics Library: ggplot2 | -- |
| September 2014 | Bioinformatics | Introduction to R Programming, Part II | Introduction to R Programming, Part II |
| August 2014 | Bioinformatics | Introduction to R Programming, Part I | Introduction to R Programming, Part I |
| July 2014 | Bioinformatics | Introduction to Python Programming, Part II | Introduction to Python, Part II |
| June 2014 | Bioinformatics | Introduction to Python Programming, Part I | Introduction to Python, Part I |
| May 2014 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | Introduction to Linux for Bioinformatics |
| April 2014 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-Seq Data with the CRI |
| March 2014 | Bioinformatics | Overview and Tutorial of Lynx: An Integrated Systems Biology Platform for Analysis of Multi-Gene Disorders | -- |
| February 2014 | Bioinformatics | Analysis of Illumina Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| January 2014 | Bioinformatics | How to Use the CRI’s Computational Infrastructure for Bioinformatics Analysis | CRI Infrastructure for Bioinformatics, Part I and Part II |
| November 2013 | Bioinformatics | Introduction to Perl: Learning by Example | Introduction to Perl |
| October 2013 | Bioinformatics | Maximizing the Biological Interpretation of Gene, Transcript, & Protein Expression Data with IPA | -- |
| September 2013 | Bioinformatics | Introduction to Python Programming | Introduction to Python Programming |
| August 2013 | Bioinformatics | Introduction to R Programming | Introduction to R Programming |
| June and July 2013 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | Introduction to Linux Command Line for Bioinformatics |
| May 2013 | Bioinformatics | Analyzing Illumina ChIP-Seq Data with the CRI | Analyzing Illumina ChIP-Seq Data with the CRI |
| April 2013 | Bioinformatics, HPC | Introduction to CRI’s HPC Cluster for Bioinformatics Computing | Introduction to CRI's HPC for Bioinformatics |
| March 2013 | Bioinformatics | Analysis of Illumina Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| February 2013 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-Seq Data |
| January 2013 | Bioinformatics | Analysis of Microarrays with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| November 2012 | Bioinformatics | Analyzing Illumina Whole Exome Data with the CRI | Analyzing Illumina Whole Exome Data with the CRI |
| September 2012 | Bioinformatics | Galaxy: Web-based Bioinformatics Analysis & RNA-Seq Workflow Management | Galaxy: Web-Based Bioinformatics Analysis |
| August 2012 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-seq Data |
| July 2012 | Bioinformatics | Analysis of Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
