Margarete A. Fabre*, José Guilherme de Almeida*, Edoardo Fiorillo, Valeria Orru, Michele Marongiu, MS Vijayabaskar, Joanna Baxter, Claire Hardy, Federico Abascal, Michael Spencer Chapman, Iñigo Martincoren, Jyoti Nangalia, Emily Mitchell, Peter Campbell, Eoin McKinney, Francesco Cucca, Moritz Gerstung, George S. Vassiliou.
* joint first authors
In this notebook, we detail the estimation of the technical overdispersion using technical replicates.
In this notebook, we validate the hierarchical Bayes model used in this work with Wright-Fisher simulations.
In this notebook, we validate the estimation of growth rates from phylogenetic trees and collect the evidence for saturation from simulations.
In this notebook, we assess whether other methods for population size estimate perform well when determining growth rates.
In this notebook, we analyse the estimates for growth rate, infer and analyse the agest at onset for all clones and analyse possible associations with phenotype.
In this notebook, we analyse the phylogenetic trees in a recent publication to further collect evidence showing that clones decelerate.
In this notebook, we finalise our analysis of historical growth effect and clonal deceleration, while also confirming there are no obvious explanations for poor fits.