The epigenetics effects of transposable elements are not restricted to gene silencing Scripts and data for the manuscript "The epigenetics effects of transposable elements are not restricted to gene silencing". Directories and files TEs with epigenetic effects data: contains table for the 2,235 polymorphic TEs analyzed Epigenetic effects: ad-hoc bash scripts to analyze the epigenetic effects of TEs Expression analyses: ad-hoc bash and R scripts to compute the z-score comparing gene expression between alleles with and without the TE insertion Obtain breakpoints: scripts to obtain the breakpoint coordinate for TEs absent from genomes Null distribution: script to select random regions of the genome that matches the location of TE insertions ANALYSES_EPIGENETICS.Rmd: R Markdown documents with the code used for doing analyses and creating figures Citation Coronado-Zamora & González (2025) The epigenetics effects of transposable elements are not restricted to gene silencing. Genome Biology. Contact Project: https://github.com/GonzalezLab/epigenetic-effects-transposons-dmelanogaster/