cfDNAPro: an R/Bioconductor package to characterise and visualise cell-free DNA biological features in liquid biopsy
Haichao Wang,Nitzan Rosenfeld,Hui Zhao,Christopher G. Smith Cancer Research UK Cambridge Institute, University of Cambridge
Abstract
Cell-free (cf) DNA enters human blood circulation by various biological processes. There is upsurging evidence that cfDNA biological features could be exploited to support sensitive cancer detection, treatment selection and minimal residual diseases detection. However, there are currently no R packages designed for automated analysis of cfDNA biological features such as fragment size, periodicity, nucleotide frequency, nucleosome occupancy etc. Here we present a Bioconductor R package, cfDNAPro, which provides a comprehensive easy-to-use framework for automated data characterisation and visualisation of cfDNA sequencing data. The cfDNAPro R package implements functions for calculating overall, median and modal fragment size distributions, calculating the peaks and troughs, as well as the periodicity of oscillations in the fragment size profile. Also, cfDNAPro includes functions depending on ggplot2 for data visualisation. As the first R package for cfDNA data characterisation, cfDNAPro increases analysis efficiency and reproducibility, we hope that it will encourage more researchers to develop further applications under the new paradigm offered by this package.
Keywords: liquid biopsy,NGS,cancer research,genomics,cell-free DNA,cfDNA,cancer early detection,translational research,fragmentomics,body fluid,plasma