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This is the development version of cfTools; for the stable release version, see cfTools.

Informatics Tools for Cell-Free DNA Study

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License file LICENSE
Imports Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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