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.
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.
Dive into basic spatial transcriptomics analysis using Partek Flow. Gain hands-on experience with data analysis workflows and visualization.
Discover the power of integrating spatial transcriptomic data with multiple data types such as single cell RNASeq using Partek Flow for comprehensive insights.
Upon completing this series, you should be able to
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.
Lecture Video :
HSLS Software Registration for PartekFlow
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 | |
Method of the Year 2020: spatially resolved transcriptomics. Nat. Methods 18, 1 (2021)
An introduction to spatial transcriptomics for biomedical research
Museum of spatial transcriptomics
Advances in spatial transcriptomics and related data analysis strategies
Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.e29 (2021)
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.