Code and Data for "Genome-wide repeat landscapes in cancer and cell-free DNA" (Annapragada et.al., Science Translational Medicine, 2024)

Code and Data for "Genome-wide repeat landscapes in cancer and cell-free DNA" 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which may be found at https://github.com/cancer-genomics/reproduce_lucas_wflow These github repositories have also been archived in this Zenodo as they were on 02/06/2024 (DELFI fragmentation) and 03/11/2024 (ARTEMIS).