TEsingle

TEsingle is a software package for including both genes and transposable elements in single-cell (or single-nucleus) RNA-seq analysis. TEsingle handles mapping, cell barcode & UMI processing, and abundance estimation. We’ve paid particular attention to differentiating unprocessed intron sequences from expressed TEs. Output is formatted as a cell count matrix suitable for downstream analysis in your favorite single-cell clustering & plotting package (like Seurat).

Github Link coming soon!