Data for: Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets

This repository contains simulated datasets and supplementary files associated with our preprint published on bioRxiv: DOI: https://doi.org/10.64898/2026.02.26.708244 The materials provided here support full reproducibility of the analyses presented in the manuscript. They include raw input data, processed outputs, and feature annotations required to replicate the benchmarking workflow. Analysis code is available on GitHub: https://github.com/ScialdoneLab/TEbenchmarking Folder Structure data/ Simulated count matrices and corresponding FASTQ files TEannotation/ Mouse and human transposable element (TE) annotation files (obtained from the Hammell Lab) whitelists/ Cell barcode whitelists and cell type annotations for cells passing quality control (QC) filtering jc_mm10.txt.tar.gz Mouse mm10 TE annotation including evolutionary distances computed with the Jukes Cantor model