Bioconductor version: Release (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>
Citation (from within R,
enter citation("cfTools")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cfTools")
HTML | R Script | cfTools-vignette |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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 |
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 |
Old Source Packages for BioC 3.17 | Source Archive |
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