# ΛΑΞΕΣΙΣ (LACHESIS)
<img align="left" src="man/figures/LACHESIS_logo.svg" alt="LACHESIS logo" width="180"></img>
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ΛΑΞΕΣΙΣ (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, ΛΑΞΕΣΙΣ tests whether there is evidence for an early common ancestor, oncogenic events acquired prior to malignant transformation. ΛΑΞΕΣΙΣ also provides modalities to compare tumor evolution across patient collectives, and to correlate evolutionary timings with outcome. Please refer to our [vignette](/vignettes/vignette_LACHESIS.Rmd) for further information.
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## Documentation
A [vignette](vignettes/vignette_LACHESIS.Rmd) explaining how to use ΛΑΞΕΣΙΣ, input and output formats alongside with example data can be installed by setting `build_vignettes = TRUE` and `dependencies = TRUE`.
## Demo
Please refer to our [vignette](vignettes/vignette_LACHESIS.Rmd) for an example analysis with ΛΑΞΕΣΙΣ.
## System requirements
### Hardware requirements
ΛΑΞΕΣΙΣ runs on a standard computer.
### Software requirements
#### OS Requirements
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
#### R dependencies
ΛΑΞΕΣΙΣ 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).
## Version
0.99.0
## Citation
Körber et al., Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome, *Nature Genetics* **55**:619-630 (2023).
## Installation
```r
devtools::install_github("VerenaK90/LACHESIS")
````
To install the vignette, run
```r
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.
## License
ΛΑΞΕΣΙΣ is run under an **GPL (>= 3)** License.
## Contact
Verena Körber (verena.korber@ndcls.ox.ac.uk), Anand Mayakonda (a.mayakonda@kitz-heidelberg.de), Maximilia Eggle (maximilia.eggle@kitz-heidelberg.de).
