DOI: 10.18129/B9.bioc.cfTools  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see cfTools.

Informatics Tools for Cell-Free DNA Study

Bioconductor version: 3.17

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>

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biocViews BiomedicalInformatics, DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License file LICENSE
Imports Rcpp, utils, GenomicRanges, basilisk, R.utils
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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