ΛΑΧΕΣΙΣ (LACHESIS) is an R package to infer tumor evolution during malignant tranformation from bulk whole genome sequencing data. It uses single nucleotide variants and (ideally allele-specific) copy number information as input to compute mutation densities at clonal chromosomal gains and at the tumor's most recent common ancestor. Additionally, ΛΑΧΕΣΙΣ tests whether there is evidence for an early common ancestor, oncogenic events acquired prior to malignant transformation. ΛΑΧΕΣΙΣ also provides modalities to compare tumor evolution across patient collectives, and to correlate evolutionary timings with outcome. Please refer to our vignette for further information.
A vignette explaining how to use ΛΑΧΕΣΙΣ, input and output formats alongside with example data can be installed by setting build_vignettes = TRUE and dependencies = TRUE.
Please refer to our vignette for an example analysis with ΛΑΧΕΣΙΣ.
ΛΑΧΕΣΙΣ runs on a standard computer.
This package is supported for macOS, Windows and Linux. The package has been tested on the following systems:
MacBook Pro: Sonoma (14.6.1) Windows 10, Version 22H2
ΛΑΧΕΣΙΣ was tested on R v4.5.1 and requires installation of the packages data.table (1.15.4), ggplot (≥3.5.1), tidyr (1.3.1), vcfR (1.15.0).
0.99.0
Körber et al., Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome, Nature Genetics 55:619-630 (2023).
devtools::install_github("VerenaK90/LACHESIS")
To install the vignette, run
devtools::install_github("VerenaK90/LACHESIS", build_vignettes = TRUE, dependencies = TRUE)
The vignette can then be viewed by typing vignette("vignette_LACHESIS", "LACHESIS"). The package including its vignette can be installed within a few minutes.
ΛΑΧΕΣΙΣ is run under an GPL (>= 3) License.
Verena Körber (verena.korber@ndcls.ox.ac.uk), Anand Mayakonda (a.mayakonda@kitz-heidelberg.de), Maximilia Eggle (maximilia.eggle@kitz-heidelberg.de).