Frequency Analysis of Sequence Data (FASD)

Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.

A motif discovery and characterization program based on mutual information.

A motif discovery and characterization program for proteins based on mutual information.

Uses copy number and mutation data from a cohort of patients, for example from TCGA, to find modules of genes with a related mutation pattern.

An algorithm for discovering long shared segments of identity by descent (IBD) between pairs of (unrelated) individuals in a large population.

Provides an integrated suite of genomics tools.

HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data.

A tool for calling amplified alleles and constructing the amplified haplotype within called tumor amplicons.

Predicts competing endogenous RNA (ceRNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information.

A method for inferring per-locus human leukocyte antigen types using shared segments that are identical by descent (IBD), inferred from genotype data.

A method to infer cancer somatic mutation hotspots.

A tool for constructing modules regulated by eQTLs using gene expression and SNP variation data across multiple individuals.

A tool for selecting individual for sequencing by total information potential, based on GERMLINE output.

A functional and categorical enrichment program based on mutual information.