CellRanger-TE
CellRanger-TE is a modification to the Cell Ranger analysis pipeline that enables the quantification of genes and transposable elements from single-cell and single-nucleus datasets using the CellRanger software package.
It takes GENCODE FASTA and gene annotations, filters them according to the instructions provided by 10x Genomics regarding reference databases, and adds customized TE annotations to create a TE-aware reference database.
This is currently only available for mouse (GRCm39) and human (GRCh38).
Requirements
Please check our GitHub repository to download the script and for information on additional software required.
Citation
O'Neill K, Shaw R, Bolger I; NYGC ALS Consortium; Tam OH, Phatnani H, Gale Hammell M. (2025) ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers. Cell Rep. Mar 10;44(3):115402. PMID: 40067829