Citation:
Annapragada, A.V. Niknafs, N. White, J.R. Bruhm, D.C., Cherry, C., Medina, J.E., Adleff, V., Hruban C., Mathios, D., Foda, Z.H., Phallen, J., Scharpf, R.B., Velculescu, V.E. Genome-wide repeat landscapes in cancer and cell-free DNA. Science Translational Medicine. 2024.

The code to run the ARTEMIS pipeline and reproduce manuscript figures is publicly available at  https://github.com/cancer-genomics/artemis2024

This code also depends on code that generates DELFI features for fragmentation-based analysis, which may be found at   https://github.com/cancer-genomics/reproduce_lucas_wflow 

These github repositories have also been archived in this Zenodo as they were on 02/06/2024 (DELFI fragmentation) and 03/11/2024 (ARTEMIS).