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Informatics Tools for Cell-Free DNA Study

Bioconductor version: Release (3.18)

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 ucla.edu>

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


To install this package, start R (version "4.3") 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 1.2.0
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
URL https://github.com/jasminezhoulab/cfTools
Bug Reports https://github.com/jasminezhoulab/cfTools/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To Rcpp, BH
Depends On Me
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Package Archives

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

Source Package cfTools_1.2.0.tar.gz
Windows Binary cfTools_1.2.0.zip
macOS Binary (x86_64) cfTools_1.2.0.tgz
macOS Binary (arm64) cfTools_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cfTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cfTools
Bioc Package Browser https://code.bioconductor.org/browse/cfTools/
Package Short Url https://bioconductor.org/packages/cfTools/
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