Software

∗∗∗ We listed some previous and ongoing projects. Please contact us if you need more information or support.

  • DrVAEN
    Drug response prediction through deep Variational Autoencoder model followed by Elastic Net.
  • INSCT
    Integrating millions of single cells using batch-aware triplet neural networks.
  • Cao_RNA-seq data
    RNA-seq data from the mouse pancreas with cerulein-induced chronic pancreatitis.
  • CSEA-DB
    Cell-type-Specific Enrichment Analysis DataBase.
  • KinaseMD
    Kinase mutations and drug responses.
  • Deep4mC
    A deep learning method for systematic assessment and computational prediction of DNA N4-methylcytosine sites.
  • DeepFun
    A tissue and cell type specific deep learning sequence-based model to decipher noncoding variant effects.
  • DrivAER
    Identification of driving transcriptional programs in single-cell RNA sequencing data.
  • 6mA-Finder
    Computational prediction of 6mA sites in the DNA sequences.
  • TSEA-DB
    A trait-tissue association map for human complex traits and diseases.
  • VISDB
    A knowledgebase containing the most comprehensive DNA virus integration sites and also the integration sites for several typical RNA retrovirus.
  • CleftGeneDB
    the cleft gene annotation database aiming to provide a resource or reference for the midfacial development and the related disease studies for mouse and human.
  • MotifPredictor
    With miRNA-TF, miRNA-gene, TF-miRNA, and TF-gene interactions as input, this C package can identify specific motifs (miRNA-TF-gene feed-forward and feedback loops) from networks.
  • ANCO-GeneDB
    annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence.
  • deTS
    An R package to identify the most relevant tissues for candidate genes or for gene expression profiles.
  • CNet
    A JAVA package that detects groups of genomic signatures that are associated with clinical and phenotypical outcomes.
  • TissGDB
    Tissue-specific Gene annotation DataBase in cancer for better understanding tissue-specificity and identifying targetable alterations of tissue-specific genes.
  • scRNASeqDB
    A database for gene expression profiling in human single cell by RNA-seq.
  • <SZGR
    Schizophrenia Gene Resource provides a comprehensive online resource for schizophrenia genetics studies.
  • mutLBSgeneDB: mutated Ligand Binding Site gene DataBase
    mutLBSgeneDB is the first database encompassing comprehensive annotations for all genes having ligand binding site mutations. mutLBSgeneDB may contribute to systematic analysis for functional annotations of genes with ligand binding site mutations for cancer and drug research in the precision medicine era.
  • ccmGDB: Cancer Cell Metabolism Gene Database.
    A comprehensive database for cataloging cancer cell metabolism genes for better understanding of mutational landscapes of all metabolism genes and identifying potential druggable cancer cell metabolism targets in cancerous cells.
  • TSGene 2.0: Tumor Suppressor Gene Database version 2.0 
    A comprehensive database for tumor suppressor genes in multiple model organisms and their related biological information (tumor types, gene expression, mutations, pathways, protein-protein interactions, and non-coding genes, etc). Major updates include: added and curated hundreds more TSGenes (1022 coding and 192 non-coding genes now), added pan-cancer gene expression, somatic mutation, miRNA data, added many pre-computed results (e.g. differential expression, mutation hotspots, networks, loss of function), data visualization, among others.
  • EW_dmGWAS 
    Edge-weighted dense module search for genome-wide association studies and gene expression profiles. This is an upgraded algorithm of our previous dmGWAS to boost GWAS signals in a node- and edge-weighted protein-protein interaction network. In EW_dmGWAS, we utilize condition-specific gene expression profiles for edge weights.
  • CCG
    The Catalogue of Cancer Genes database is an integrated Interactome of Cancer Genes.
  • KinomeNetworkX
    A Network Atlas of 538 Human Kinase genes.
  • DESnowball
    Method to identify downstream target genes that are affected by a recurrent driver mutation.
  • PAHKB
    Pulmonary Arterial Hypertension KnowledgeBase.
  • VirusFinder
    Software to detect viruses and their integration sites in host genomes through next generation sequencing data.
  • CNVannotator
    A comprehensive annotation server for copy number variation (CNV) in humans.
  • TSGene: Tumor Suppressor Gene Database
    A comprehensive database for tumor suppressor genes in multiple model organisms and their related biological information (tumor types, gene expression, mutations, pathways, protein-protein interactions, and non-coding genes, etc).
  • VarWalker
    Mutation network analysis of putative cancer genes from NGS data
  • NGS Catalog
    A Database of Next Generation Sequencing Studies in Humans
  • DTome
    a web-based tool for drug-target interactome construction
  • GenRev
    a Python package for subnetwork extraction
  • DT tool (Drug-target extraction tool in Python)
    source code, examples, and documents can be downloaded here.
  • glad (gene length bias detection in GWAS datasets)
    source code to detect gene length bias as in Jia et al.
  • ERGR
    Ethanol Related Gene Resource
  • InPrePPI
    A web-based application for the prediction of protein-protein interactions (PPIs) using one of the four genomic context based methods (Phylogenetic profile method, Gene cluster method, Gene fusion method, and Gene neighbor method) or an integration method (InPrePPI) based on these four methods.
  • SNPKS
    A statistical method to estimate the effective SNP size in vertebrate genomes.
  • Suppl. for Genomics (2004) 84:785-795
    "The influence of neighboring nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs" .
  • SNPMiner
    A SNP database and web interface with the functionalities including search, candidate SNP selections, and genetic analysis.
  • SNPNB
    A user-friendly application for analyzing the neighboring-nucleotide compositions and bias patterns of SNPs. It also evaluates statistically the effective size of SNPs which to represent the same patterns observed in a genome or on a chromosome. More functions will be added in the later versions.
  • SNPPEB 
    A web based SNP information processing and primer design application. It will parse compressed XML file from NCBI website and display SNP info as required by lab molecular biologists. It will also design primers for selected SNPs and give user-friendly output. This application will automate related lab work and release biologists from some tedious manual work.
  • Warfarin PGx
    (under construction) A warfarin database and web interface with the functionalities including search patient information and prediction of initial warfarin dose amount.
  • Lab Supports
    Phase2 Data Conversion This Perl script converts the data in tab-delimited format to Phase2 compatible format.