CCA Algorithm to Infer Regulatory Interactions

A canonical correlation analysis based algorithm that utilizes DNA methylation, copy number alteration, gene expression datasets from cancer samples to infer regulatory interactions between genes.

Gene centric methylation

A feature selection algorithm to find most predictive methylation probes for gene expression.

Gene Set Enrichment and Projection Display

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

FastMEDUSA

FastMEDUSA is a parallel program to infer gene regulatory networks from gene expression and promoter sequences. It is the parallelized version of MEDUSA (Kundaje, et al. 2008 Plos Comp. Bio.)

FMTP: Fingerprint-based Minimal Tiling Path

FMTP is a software tool to compute the MTP of a physical map based purely on restriction fingerprint data (and the contigs). FMTP completely ignores the ordering of clones obtained by the physical map algorithm.

Compartmentalized Assembler

Compartmentalized assembler is a novel method for the assemlby of high quality physical maps from fingerprinted clones. Our method exploits the presence of genetic markers at the genomic level that allows us to pre-cluster the clones. For each cluster of clones, a local physical map is first constructed. Then, all the individual maps are carefully merged into the final physical map.