CellTree is an open-source R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data, using Latent Dirichlet Analysis and dedicated tree-building heuristics.
Develop new statistical methods for cancer science.
We designed a Regularisation-path algorithm that uses patterns of input variables (itemsets) as covariates to fit a Cox Proportional Hazards regression model. Full description of method and algorithm published in Oxford Journal's Bioinformatics (based on work by Park & Hastie (2006): L1 Regularization Path Algorithm for Generalized Linear Models).
The entire source code (in R) for this project, can be found on a public GitHub repository.