Life Science Data Analytics
and Algorithmic Bioinformatics
Software

GOSim (Bioconductor)

computation of information theoretic Gene Ontology similarities between terms and gene products; GO enrichment analysis

gene2pathway (Bioconductor)

predicting KEGG Pathway membership for individual genes via protein domains signatures using hierarchical classification

nem (Bioconductor)

reverse engineering / structure learning of biological networks from high dimensional intervention effects

pathClass (CRAN)

patient classification using gene expression data and network information

netClass (CRAN)

patient classification using mRNA + optionally miRNA data and network information; some plotting functionalities

birta (Bioconductor, deprecated)

Bayesian prediction of TF and miRNA activities from joint gene and miRNA expression data.

birte (Bioconductor, replaces birta)

Bayesian prediction of TF and miRNA activities from different expression data entities; interfaces nem for gene regulatory network inference.

SteinerNet (CRAN archive, deprecated)

Calculation of Steiner trees on large biological networks using several heuristic algorithms.

Tropical Equilibration

Algebraic method for ordering variables in biochemical networks according to velocity.

Linking Metabolic Network Features to Phenotypes using Sparse Group Lasso