cfTools
Informatics Tools for Cell-Free DNA Study
Bioconductor version: Release (3.19)
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 | 1.4.0 |
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_1.4.0.tar.gz |
Windows Binary | cfTools_1.4.0.zip (64-bit only) |
macOS Binary (x86_64) | cfTools_1.4.0.tgz |
macOS Binary (arm64) | cfTools_1.4.0.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 |