plasmut
Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic
Bioconductor version: 3.24 · Package version: 1.11.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("plasmut")Details
| Maintainer | Adith Arun <adith.3.arun@gmail.com> |
| Author | Adith Arun [aut, cre], Robert Scharpf [aut] |
| License | Artistic-2.0 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, GermlineMutation, Sequencing, Software, SomaticMutation |
| Package Short Url | https://bioconductor.org/packages/plasmut/ |
Citation
From within R, enter citation("plasmut"):
Adith Arun, Robert Scharpf. plasmut: Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic. doi:10.18129/B9.bioc.plasmut, R package version 1.11.0, https://bioconductor.org/packages/plasmut.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | plasmut_1.11.0.tar.gz |
| Windows binary (x86_64) | plasmut_1.11.0.zip |
| macOS binary (arm64) | plasmut_1.11.0.tgz |
| macOS binary (x86_64) | plasmut_1.11.0.tgz |