This is the development version of cfTools; for the stable release version, see cfTools.
Informatics Tools for Cell-Free DNA StudyBioconductor version: Development (3.22)
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] ORCID: 0000-0002-0563-8957 , Mary Louisa Stackpole [aut] ORCID: 0000-0003-4432-6718 , Shuo Li [aut] ORCID: 0000-0002-1960-6016 , Xianghong Jasmine Zhou [aut] ORCID: 0000-0002-4522-7490 , Wenyuan Li [aut] ORCID: 0000-0002-5029-8525
Maintainer: Ran Hu <huran at ucla.edu>
Citation (from within R, entercitation("cfTools")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("cfTools")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cfTools")Follow Installation instructions to use this package in your R session.
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