Computational models and data analysis tools

Time series data analysis

Batch analysis of phenotypic microarray data (also known as BIOLOG): Code
Bayesian inference for generalized Lotka-Volterra models: Code

Multiomics data analysis

Pipeline for short-read genomic sequencing data analysis (SNVs, CNVs, aneuploidy): Code
Pipeline for RNA-sequencing data analysis: Code

Metabolic flux analysis

Reconstruction of genome-scale metabolic models from whole-genome sequencing data: Code

Machine learning models

Tutorial codes for popular machine learning models: Code