Repository of the scripts used in Brückner, L., Xu, R., Tang, J. et al. Micronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival. Nat Genet (2026). https://doi.org/10.1038/s41588-026-02782-w

Single micronucleus sequencing analysis (includes code for preprocessing, analysis and plotting; includes preprocessed raw files and plots)

single_micronucleus_seq

RNA sequencing analysis (includes code for processing, analysis and plotting; includes raw count data)

RNAseq

ChIPseq plotting (includes code for processing, plotting)

ChIPseq

Nanopore replication fork analysis (includes code for processing, analysis and plotting)

nanopore

This code has been tested on aarch64-apple-darwin20 (64-bit) running under: macOS Monterey 12.3.

Raw data for this study has been deposited to ArrayExpress under accessions E-MTAB-16933 (RNAseq), E-MTAB-16944 (ChIPseq) and ENA under accessions PRJEB112294 (single micronucleus sequencing) and PRJEB111610 (nanopore).