Chapter 3 Generate gene expresion matrix

In this chapter, we will generate the gene expression matrix, genes by cells, from multiple input formats commonly used in single-cell RNA sequencing, including sparse matrix by 10x Genomics, text-table file, HDF5 file by 10x Genomics and H5AD file.

For demonstration purposes, scMINER embedded four datasets in extdata/demoData_readInput, with one for each input format. All of these four samples were generated by downsampling the real scRNA-seq data.