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 (3.24)
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("plasmut")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GermlineMutation, Sequencing, Software, SomaticMutation |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0) |
| Imports | tibble, stats, dplyr |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) |
| Linking To | |
| 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 | plasmut_1.11.0.tar.gz |
| Windows Binary (x86_64) | plasmut_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | plasmut_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | plasmut_1.11.0.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 |