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- TADsplimer (in press at Genome Biology): A bioinformatic toolkit to identify the TAD splits and merges between Hi-C samples.
- CEFCIG at GitHub or GoogleSite(Manuscript submitted): A Computational Epigenetic Framework for Cell Identity Gene discovery.
- GridGO: a grid-based genetic algorithm for automatic optimization of epigenetic signature analysis on the basis of biological significance.
- CIGdiscover: a logistic regression model for cell identity genes discovery
- CIGnet: a novel network method to uncover master transcription factors for cell identity genes in an unbiased, knowledge-guided, and quantitatively testable manner.
- CIGDB: A Cell Identity Gene Database.
- CAGRE (Science, 2019): A bioinformatic tool for Commulative Analysis of Genomic Region Enrichment.
- FAID (Nature, 2018): A bioinformatic tool for Feature Analysis of Inserted DNA in a genome.
- DANPOS2 (Nature Genetics, 2015): a set of 8 bioinformatics tools, including:
- Dpos: comparative analysis of MNase-Seq data between samples.
- Dpeak: comparative analysis ChIP-Seq data between samples.
- Dregion: analyzing broad epigenetic domains, e.g., super enhancers.
- Stat: statistical analysis of positions, peaks, or regions defined by DANPOS.
- Selector: mapping positions, peaks, or regions to any given genomic features such as genes.
- Profile: analyzing epigenetic signal at any given genomic regions, e.g., genes, enhancers.
- Wiq: a tool for genome wide quantile normalization of epigenetic data.
- Wig2Wiq: a tool for converting wiggle format file to wiq format.
- DANPOS (Genome Research, 2013): A tool for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing
- SpikeSCN (Genes & Development, 2013). Genome structure and copy number variation analysis based on genome sequencing with spike-in control.
- BarVar (Cell reports, 2013). A bioinformatics pipeline to screen for drug-resistant genetic variations from barcode sequencing data.
- NucHMM (GPB, 2010). A Hidden Markov Model for nucleosome positioning prediction based on DNA sequence feature.
- GenomePSD (Nucleic acids research, 2008). A Power Spectrum Density analysis tool for genome sequence.