Registration Open for Bioc2024 July 24-26


Informatics Tools for Cell-Free DNA Study

Bioconductor version: Release (3.19)

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

Author: Ran Hu [aut, cre] , Mary Louisa Stackpole [aut] , Shuo Li [aut] , Xianghong Jasmine Zhou [aut] , Wenyuan Li [aut]

Maintainer: Ran Hu <huran at>

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


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:

cfTools-vignette HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License file LICENSE
Imports Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData
System Requirements
Bug Reports
See More
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To Rcpp, BH
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 cfTools_1.4.0.tar.gz
Windows Binary
macOS Binary (x86_64) cfTools_1.4.0.tgz
macOS Binary (arm64) cfTools_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats