Bioc2026 Registration Open!

LACHESIS

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

Bioconductor version: 3.23 · Package version: 1.0.0

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.

Installation

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

BiocManager::install("LACHESIS")

Details

MaintainerVerena Körber <verena.korber@ndcls.ox.ac.uk>
AuthorVerena Körber [aut, cre] (ORCID: <https://orcid.org/0009-0005-3888-2648>), Anand Mayakonda [aut], Maximilia Eggle [aut]
LicenseGPL (>= 3)
URLhttps://github.com/VerenaK90/LACHESIS
Bug Reportshttps://github.com/VerenaK90/LACHESIS/issues
Downloads rank85
Source branchRELEASE_3_23
biocViewsSequencing, Software, SomaticMutation, StatisticalMethod, Survival, TimeCourse, WholeGenome

Documentation

Download

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