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ctDNAtools: An R package to work with sequencing data of circulating tumor DNA
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ctDNAtools: An R package to work with sequencing data of circulating tumor DNA
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Paper
ctDNAtools: An R package to work with sequencing data of circulating tumor DNA
2020
Overview
Sequencing of cell-free DNA (cfDNA) including circulating tumor DNA (ctDNA) in minimally-invasive liquid biopsies is rapidly maturing towards clinical utility for cancer diagnostics. However, the publicly available bioinformatics tools for the specialized analysis of ctDNA sequencing data are still scarce. Here, we present the ctDNAtools R package, which provides functionalities for testing minimal residual disease (MRD) and analyzing cfDNA fragmentation. MRD detection in ctDNAtools utilizes a Monte Carlo sampling approach to test ctDNA positivity through tracking a set of pre-detected reporter mutations in follow-up samples. Additionally, ctDNAtools includes various functionalities to study cfDNA fragment size histograms, profiles and fragment ends patterns. Availability: The ctDNAtools package is freely available under MIT license at https://github.com/alkodsi/ctDNAtools.
Publisher
Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
Subject
