I am trying to convert the digital expression matrix of a single cell RNA-seq dataset on GEO to a counts matrix (e.g. rows = genes, columns = samples, data = gene counts) and was wondering if anyone knew how to do that.
Try the function Matrix::readMM from the Matrix package in R. It reads the MatrixMarket (mtx) files which are the counts. The barcodes, features etc you can read with any reader function, e.g. read.delim.
You will then have to assemble the data pbject you want, so putting features as rownames and barcodes as colnames. There are container formats for single-cell data, e.g. the SingleCellExperiment class in Bioconductor that might be worth reading about, which can also store dimensionality reductions, metadata etc.