VisiumIO: Working with 10X Genomics Visium Data

Author(s): Marcel Ramos Pérez

Affiliation(s): CUNY School of Public Health, New York, N.Y., USA



Bioconductor’s approach to re-using existing classes enables the growth of the software ecosystem. We make use of the BiocIO and TENxIO frameworks to work with and represent 10X Visium data. The VisiumIO package provides functions that import 10X Visium and 10X Visium HD data from the Space Ranger pipeline. We strive to make user-friendly functions and welcome feedback from the community. We will cover some of the details that enable the re-use of the BiocFile and TENxFile classes. We will cover essential import functions and basic functions to work with SpatialExperiment class objects.