Registration Open for Bioc2024 July 24-26


Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Bioconductor version: Release (3.19)

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

Author: Pitithat Puranachot [aut, cre]

Maintainer: Pitithat Puranachot <pitithat at>

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


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:

cfdnakit vignette HTML R Script
Reference Manual PDF


biocViews CopyNumberVariation, Sequencing, Software, WholeGenome
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Depends R (>= 4.3)
Imports Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang
System Requirements
Bug Reports
See More
Suggests rmarkdown, knitr, roxygen2, BiocStyle
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cfdnakit_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) cfdnakit_1.2.0.tgz
macOS Binary (arm64) cfdnakit_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats