cfTools
This is the development version of cfTools; for the stable release version, see cfTools.
Informatics Tools for Cell-Free DNA Study
Bioconductor version: Development (3.23)
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 "4.6") 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.
Documentation
| Reference Manual |
Details
| biocViews | BiomedicalInformatics, DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Sequencing, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 years) |
| License | file LICENSE |
| Depends | |
| Imports | Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData, grDevices, graphics |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/cfTools/ |
| Package Downloads Report | Download Stats |