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plasmut

This is the development version of plasmut; for the stable release version, see plasmut.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("plasmut")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Bayesian, GermlineMutation, Sequencing, Software, SomaticMutation
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports tibble, stats, dplyr
System Requirements
URL
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Suggests knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0)
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Enhances
Depends On Me
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Package Archives

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

Source Package plasmut_1.1.0.tar.gz
Windows Binary plasmut_1.1.0.zip
macOS Binary (x86_64) plasmut_1.1.0.tgz
macOS Binary (arm64) plasmut_1.1.0.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/
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