genefu

genefu provides algorithms for gene expression–based molecular subtyping and prognosis prediction in breast cancer studies.

Key Features:

• Molecular Subtyping: Implements algorithms to classify breast tumors into molecular subtypes from gene expression profiles.
• Prognostication Algorithms: Provides algorithms to estimate patient prognosis based on gene expression signatures.
• Gene Expression Signatures: Incorporates published gene signatures for association with breast cancer subtypes and outcomes.
• Reimplementation of Algorithms: Reimplements published molecular classification and prognosis algorithms to support comparison and reproducibility.
• Gene Mapping Across Platforms: Supports gene mapping between different microarray platforms to enable cross-platform analyses.
• Gene Selection and Survival Analysis: Implements gene selection methods and survival analysis to assess the impact of gene profiles on patient outcomes.

Scientific Applications:

• Breast Cancer Research: Applied to study molecular heterogeneity, assign subtypes, and predict prognosis from expression data in breast cancer cohorts.
• Comparative Studies: Used to reimplement and compare published classifiers and signatures across datasets and platforms for validation.

Methodology:

genefu is implemented in R/Bioconductor as a multi-tiered compendium integrating various published bioinformatics algorithms.