Chapter 2 Visium data preprocessing
Here, we describe several detailed data preprocessing steps for 10x Genomics Visium data. These steps are required to prepare raw data files to load the data into R for further computational analysis.
In the examples shown here, we use the Space Ranger and Loupe Browser software provided by 10x Genomics to preprocess Visium data. Alternative preprocessing workflows have also been developed by others, including the alevin-fry pipeline for Visium and other platforms.