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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Workshop description

Register and join our comprehensive Workshop Series: Spatial Transcriptomic Analysis with Partek flow to gain a deep understanding of spatial transcriptomics analysis. This three-part series, leveraging Partek Flow software, will cover the entire workflow, from data import, pre processing to results interpretation and visualization.

Register for Workshop 1: Introduction to Spatial Transcriptomics technologies and Partek Flow

Explore the fundamentals of spatial transcriptomics technologies and Partek Flow software. Learn how to seamlessly transition from raw data to generate spatial count data using 10x Cloud as well as Partek flow.

Register for Workshop 2: Basic Spatial Transcriptomic Analysis using Partek Flow

Dive into basic spatial transcriptomics analysis using Partek Flow. Gain hands-on experience with data analysis workflows and visualization.

Register for Workshop 3: Advanced  Spatial Transcriptomic Analysis using Partek Flow

Discover the power of integrating spatial transcriptomic data with multiple data types such as single cell RNASeq using Partek Flow for comprehensive insights.

Objectives

Upon completing this series, you should be able to

  • Describe the spatial transcriptomics technologies and data analysis pipelines
  • Use Partek Flow software for analyzing and visualizing spatial transcriptomics data
  • Perform spatial transcriptomic analysis and visualization 
  • Integrate spatial transcriptomics data with other omics data types such as single cell transcriptomic data

Target Audience

Experimental biologists seeking to analyze spatial transcriptomic data generated through experiments or retrieved from public datgabases. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so no programming experience is required.

Workshop Material

Week 1 Introduction to Spatial Transcriptomics and Partek Flow

  • Datasets and Powerpoint : Workshop 1 Materials
  • Lecture Video : 

Week 2 : Basic Spatial Transcriptomic Analysis with using Partek Flow
  • Datasets and Powerpoint : Workshop 2 Materials
  • Lecture Video : 
Week 3 : Advanced Spatial Transcriptomic Analysis Using Partek Flow
  • Datasets and Powerpoint : Workshop 3 Materials
  •  Lecture Video : 

Software Registration

HSLS Software Registration for PartekFlow

Additional Resources

Documentation : 
Databases Tools
10X Genomics - Spatial Transcriptomics - 10x Genomics spatial Transcriptomics database Space Ranger - a set of 10x genomics analysis pipelines for spacial transcriptomic data
Cell Marker - a manually curated resource of cell markers in human and mouse Azimuth - a tool for rapid mapping of query datasets to references
Panglao db - a database for single cell RNA seq experiments from mouse and human Garnett - a tool for automated cell type classification
Single Cell Portal (Broad Institute) -  portal that contains an analysis of human glioma, immune, and other stromal cells at the single cell level STtools - a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data
SpatialDB - a database for spatially resolved transcriptomes  
STOmicsDB - a comprehensive database for spatial transcriptomics data sharing, analysis and visualization  
   

 

Attribution

 

Please include the following statement in the acknowledgments section for all publications, posters, and presentations:

[software name, such as Partek Flow ] software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.

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