decoil.md

1. Decoil development

1.1 Decoil

Decoil implementation for reconstructing ecDNA structure heterogeneity from sequencing data is available freely on Github https://github.com/madagiurgiu25/decoil-pre.
Decoil 1.1.2-slim release available on https://doi.org/10.5281/zenodo.10785693.

1.2 Decoil-viz

Decoil-viz for visualizing the amplicon threads and summarize the genomic regions on the amplicon is available on Github https://github.com/madagiurgiu25/decoil-viz.
Decoil-viz 1.0.3 release available on https://doi.org/10.5281/zenodo.10785693.

1.3 Linear models comparison to deconvolve ecDNA elements from simulated overlapping fragments data

Simulation of overlapping ecDNA elements and reasoning of choosing LASSO model over other linear models for the likely ecDNA candidates selection.

../lasso_experiments/4_Decoil_Dev_2.ipynb