cfTools
Informatics Tools for Cell-Free DNA Study
Bioconductor version: Release (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 ucla.edu>
citation("cfTools")):
Installation
To install this package, start R (version "4.4") 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")| cfTools-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | file LICENSE |
| Depends | |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cfTools_1.6.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | cfTools_1.6.0.tgz |
| macOS Binary (arm64) | cfTools_1.6.0.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/ |
| Package Downloads Report | Download Stats |