SCIΦER is an R package that provides functions to compute expected values of the site frequency spectrum of somatic variants generated by dividing tissues that are either expanding or homeostatic. Modalities for both, neutrally evolving tissues and tissues with selection of a single clone are provided. The computations assume deterministic cell numbers in the tissue overall but account for the stochasticity of clonal growth at the level of individual clones, using clone size distributions generated by linear birth-death processes.
SCIΦER also provides modalities to simulate these processes stochastically, using gillespie's algoirthm. In addition, it allows simulation of VAF distributions generated by bulk whole genome sequencing or by pseudo-bulk data from single-cell WGS. SCIΦER was developed as part of the study "Detecting and quantifying clonal selection in somatic stem cells" by Verena Körber et al. Please refer to the github repository Clonal_hematopoiesis for further information.
Function documentation is available in the accompanying manual SCIFER_0.0.0.9000.pdf.
An exemplary guide on how to use SCIΦER to model variant accumulation and to do parameter estimation in conjunction with pyABC is given in the accompanying vignette. Re-running this example cases should take 10-15 minutes.
SCIΦER runs on a standard computer.
This package is supported for macOS and Linux. The package has been tested on the following systems:
macOS: Monterey (12.6.3) Linux: CentOS Linux 7 (Core)
SCIΦER has been tested on R v4.2.0 and v4.2.1 and requires installation of the packages deSolve (v1.34), ape (5.6.2), phangorn (v2.10.0), phytools (v1.2.0).
SCIΦER can be run in conjunction with python3 and pyABC (?0.12.6) to estimate parameters from whole genome sequencing data.
0.0.0.9000
Körber et al., Detecting and quantifying clonal selection in somatic mosaics.
devtools::install_github("VerenaK90/SCIFER", ref="paper")
If you want to install the vignette, please ensure that you have installed python, pyABC and the R packages ggplot2, reshape2, ggridges and HDInterval. Then run
devtools::install_github("VerenaK90/SCIFER", ref="paper", build_vignettes=TRUE).
The vignette can then be viewed by typing vignette("Vignette", "SCIFER"). The package including its vignette can be installed within 10-15 minutes given that python, R and pyABC have been installed.
SCIΦER is run under an MIT License.
Verena Körber ([email protected])