vPECA:
A Variants interpretation method by Paired Expression and Chromatin Accessibility data which can identify active and active selected regulatory elements and their gene regulatory network.
TimeReg:
Time course regulatory analysis from paired gene expression and chromatin accessibility time course data.
CoupledNMF:
Coupled clustering of single cell genomic data.
PECA:
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data.
Xrare:
Xrare is a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.
Previous softwares
VarSim:
A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications.
T-SVD:
Learning regulatory programs by threshold SVD regression.
SeqMap:
A tool for mapping millions of short sequences to the genome.
GeneInterestClean:
Combining scientific and statistical significance in gen ranking in Microarray analysis.
[method]
MADS:
a tool for discovery of differential alternative splicing by exon array.
GeneBASE (has been incorporated to JETTA):
Gene-level Background Adjusted Selected probe Expression. A freely available tool for computing Affymetrix Exon array gene-level expression estimates.
MultiModule:
de novo discovery of cis-regulatory modules in multiple
species.
R-SVM:
a SVM-based method for doing supervised pattern recognition (classification) with microarray gene expression data
.
TileMap:
a tool designed for tiling array data analysis.
CisModScan: Scan for cis-regulatory modules with given motif weight matrices.
