LACHESIS

Functions used to analyze early tumor evolution from whole genome sequencing data

Bioconductor version: 3.24 · Package version: 1.1.1

Other Bioconductor versions

devel is the development version; release is the current stable one.

This package provides modalities to analyze tumor evolution from whole genome sequencing data. In particular, it provides estimates of mutation densities at genomic segments and uses these to time the origin of the tumor.

DOI: 10.18129/B9.bioc.LACHESIS

Installation

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

BiocManager::install("LACHESIS")

Details

Maintainer	Verena Körber <verena.korber@ndcls.ox.ac.uk>
Author	Verena Körber [aut, cre] (ORCID: <https://orcid.org/0009-0005-3888-2648>), Anand Mayakonda [aut], Maximilia Eggle [aut]
License	GPL (>= 3)
URL	https://github.com/VerenaK90/LACHESIS
Bug Reports	https://github.com/VerenaK90/LACHESIS/issues
Source branch	devel
Build report	Bioconductor build system, r-universe
biocViews	Sequencing, Software, SomaticMutation, StatisticalMethod, Survival, TimeCourse, WholeGenome
Package Short Url	https://bioconductor.org/packages/LACHESIS/

Citation

From within R, enter citation("LACHESIS"):

Verena Körber, Anand Mayakonda, Maximilia Eggle. LACHESIS: Functions used to analyze early tumor evolution from whole genome sequencing data. doi:10.18129/B9.bioc.LACHESIS, R package version 1.1.1, https://bioconductor.org/packages/LACHESIS.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

LACHESIS - Real-time inference of evolutionary dynamics during tumor initiation based on whole genome sequencing data

Download

Follow the installation instructions to use this package in your R session.

Source package	LACHESIS_1.1.1.tar.gz
Windows binary (x86_64)	LACHESIS_1.1.1.zip
macOS binary (arm64)	LACHESIS_1.1.1.tgz
macOS binary (x86_64)	LACHESIS_1.1.1.tgz

Dependencies

Depends: R (>= 4.3)

Imports: data.table, vcfR, tidyr, stats, utils, graphics, grDevices, ggplot2, gridExtra, survival, survminer, RColorBrewer, Biostrings

Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown, knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges, MutationalPatterns, magick