Software developed
I have been developing a variety of software related to bioinformatics, interior point methods and stochastic programming.
- hsstan: an R package for fitting Bayesian models for biomarker discovery with hierarchical shrinkage priors
- GENOSCORES: a platform (with corresponding R package) for calculating genotypic predictors of binary and quantitative phenotypes
- GeneImp: an R package for fast imputation from ultra-low coverage sequencing
- nestfs: an R package for cross-validated (nested) forward selection
- libsmps++: a C++ interface to read and solve problems in SMPS format
- hippy: an implementation of interior point methods in Python
Contributions
You may also want to check out other interesting software I worked on:
- rstantools: an R package with tools for developing of R packages interfacing with Stan
- projpred: an R package that implements projection predictive variable selection
- Stan Math library: A C++ template library for automatic differentiation at the base of Stan's statistical modelling platform
- wevid: an R package to quantify the performance of a binary classifier through weight of evidence
- spiv: a Matlab code for Sparse Bayesian Instrumental Variable analysis
- Admixmap: a C++ program to model admixture using marker genotype data
- SML (Structured Modelling Language): a structure-conveying modelling language for mathematical and stochatic programming
- OOPS (Object-Oriented Parallel Solver): a structure-exploiting parallel interior point solver
- HOPDM (Higher-Order Primal-Dual Method): a Fortran/C interior point solver