This is a small introductory of the usage of several software implementations of embedding algorithms for high-dimensional gene expression data that are often used for single cell RNA-Seq (scRNA-Seq) data analysis. Many of them are available as R packages on CRAN, Bioconductor and/or GitHub.
For illustration purposes, we checked four widely used embedding methods to a bulk RNA-Seq data set, and then to a much more complex scRNA-Seq data set obtained from the scRNAseq package.