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CausalEGM: A general causal inference framework by encoding generative modeling.
scJoint: A method integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.
Sc-compReg: A method for the comparative analysis of gene expression regulatory networks.
scDEC: A method for the scATAC-seq and multiome data clustering and embedding.
Roundtrip: Density estimation using deep generative neural networks.
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.
IDP: Isoform Detection and Prediction.
fast-opt/smooth-opt: Computationally efficient multivariate density estimation package.
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment.
SeqAlto: Fast and Accurate Read Alignment for Resequencing.
SpliceMap: Splice Junction Discovery Using RNA-Seq.
rSeq: RNA-Seq Analyzer.
JETTA: Junction and Exon array Toolkit for Transcriptome Analysis.
CisGenome: An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.

CisGenome Browser: A compact stand-alone Genome Browser.

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.
DNA-Chip Analyzer (dChip): Low-level and high-level analysis of oligonucleotide microarrays
GoSurfer: Graphical data mining tool for microarray data using Gene Ontology information
UBIC2: Scalable communication, combination, and coordination among various types of biology databases
GeneNotes: Gene-centric biological information management tool for post-experiment research
SAGE Data Analysis: SAGE data analysis tool.
CisModule: De novo discovery of cis-regulatory modules
ChipInfo: Extracting gene annotation and Gene Ontology information for microarray analysis
TightClust: A resampling based clustering method for microarray data
cDNA Microarray Analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
Gifi Array Analyzer: Analyzing microarray data with Homogeneity Analysis
  Wong Lab, Bio-X program, Stanford University |  James Clark Center, 318 Campus Drive, Stanford, CA 94305-4065