Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Teams
25 October 2022
Analysis of spatial transcriptomics datasets
Ning LiuWEHI Bioinformatics
Resolving the spatial distribution of RNA in tissues is a challenge in the field of spatial biology. The development of different types of spatial transcriptomics (ST) technologies allows investigations of the spatially resolved transcriptome at different scale and different resolution. Commercial spatial technology companies like Nanostring (GeoMX and CosMX) and 10x Genomics (Visium and Xenium) provide high resolution spatial assay platforms which offer more accessible ways for researchers to understand the spatially resolved transcriptomes. However, data generated from these platforms may exhibit different characteristics as compared to traditional RNA-seq or scRNA-seq. In this talk, I'll discuss my experience in analyzing both the GeoMx and CosMx datasets and present the package standR I’ve developed for helping the analysis of ST datasets.