The software tools here were developed in the Zhang lab over many years by grant support from NSF, NIH, The Alzheimer's Association and Monsanto Corporation.
miRvial
A computational method and software package for detecting and characterizing microRNAs of diverse genomic origins
(
software)
BlocBuster
An allele-specific and network-based GWAS method
(
paper1,
paper2,
software)
mgRF
Module-guided Random Forests for integration of genotypic variation and gene expression for analyzing complex traits
(
paper,
software)
Qcut and HQcut
Finding communities in networks; also with scripts for visualizing clustering results and for constructing and clustering gene co-expression networks
(
paper1,
paper2,
software)
WordSpy
A steganalysis-based, genome scale motif finding method (software)
Rearrangement clustering
A method with application to gene expression analysis
(
paper,
software)
DBTree
A bi-directional regression tree approach to modeling transcriptional regulation
(
paper,
software)
Iterated loop matching
A method for RNA folding with pseudonots
(
software)
Degenerate multiple PCR primers
A method for selecting degenerate multiple PCR primers
(
software)
Cut-and-solve for the ATSP
Backbone guided WalkSAT
A method with dynamic noise strategy for SAT and Max-SAT
(
software)