cfTools

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 ucla.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cfTools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cfTools")

 

HTML	R Script	cfTools-vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

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
Depends
Imports	Rcpp, utils, GenomicRanges, basilisk, R.utils
LinkingTo	Rcpp, BH
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/jasminezhoulab/cfTools
BugReports	https://github.com/jasminezhoulab/cfTools/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cfTools_1.0.0.tar.gz
Windows Binary	cfTools_1.0.0.zip
macOS Binary (x86_64)	cfTools_1.0.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats