Software | Wong Lab | Stanford University

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 on GitHub