plasmut

DOI: 10.18129/B9.bioc.plasmut  

Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic

Bioconductor version: Release (3.18)

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.

Author: Adith Arun [aut, cre], Robert Scharpf [aut]

Maintainer: Adith Arun <adith.3.arun at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("plasmut")

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("plasmut")

 

HTML	R Script	Modeling the origin of mutations in a liquid biopsy: cancer or clonal hematopoiesis?
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, GermlineMutation, Sequencing, Software, SomaticMutation
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.3.0)
Imports	tibble, stats, dplyr
LinkingTo
Suggests	knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	plasmut_1.0.0.tar.gz
Windows Binary	plasmut_1.0.0.zip
macOS Binary (x86_64)	plasmut_1.0.0.tgz
macOS Binary (arm64)	plasmut_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/plasmut
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/plasmut
Bioc Package Browser	https://code.bioconductor.org/browse/plasmut/
Package Short Url	https://bioconductor.org/packages/plasmut/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive