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cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Bioconductor version: Release (3.19)

cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.

Author: Haichao Wang [aut, cre], Hui Zhao [ctb], Elkie Chan [ctb], Christopher Smith [ctb], Tomer Kaplan [ctb], Florian Markowetz [ctb], Nitzan Rosenfeld [ctb]

Maintainer: Haichao Wang <hw538 at>

Citation (from within R, enter citation("cfDNAPro")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

cfDNAPro Tutorial HTML R Script
Reference Manual PDF


biocViews Sequencing, Software, Visualization, WholeGenome
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.1.0), magrittr (>= 1.5.0)
Imports tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools(>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38
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Suggests scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat
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Follow Installation instructions to use this package in your R session.

Source Package cfDNAPro_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) cfDNAPro_1.10.0.tgz
macOS Binary (arm64) cfDNAPro_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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