Published July 14, 2025 | Version v1
Software Open

GonzalezLab/epigenetic-effects-transposons-dmelanogaster: Scripts and data for the "The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing"

Authors/Creators

  • 1. Institut Botànic de Barcelona (CSIC-CMCNB)

Description

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/

Files

GonzalezLab/epigenetic-effects-transposons-dmelanogaster-v1.zip

Files (94.8 kB)

Additional details

Related works

Is supplement to
Software: https://github.com/GonzalezLab/epigenetic-effects-transposons-dmelanogaster/tree/v1 (URL)

Software

Repository URL
https://github.com/GonzalezLab/epigenetic-effects-transposons-dmelanogaster