Genefu contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
SCUDO (Signature-based ClUstering for DiagnOstic purposes) is a tool for clustering gene expression profiles for diagnostic purposes using a new type of rank-based signatures
MARQ (Microarray Rank Query) is an online microarray retrieval tool based on rank statistics. Datasets in MARQ, most of them retrieved from GEO, are processed into signatures, which are lists of genes ranked by their level of differential expression. Each dataset defines one of more of these signatures based on the possible comparisons of its constituent samples.
ChAT (Chromatin-profile Alignment followed by Tree-clustering algorithm) employs dynamic programming of combinatorial histone modification profiles to identify locally similar chromatin sub-regions and provides complementary utility with respect to existing methods.
ChromaSig is an unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.