- DANPOS (Chen et al, Genome Research, 2013): 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.
- SpikeSCN (Hu and Chen, et al, Genes & Development, 2013). Genome structure and copy number variation analysis based on genome sequencing with spike-in control.
- BarVar ( Huang and Chen, et al, Cell reports, 2013). A bioinformatics pipeline to screen for drug-resistant genetic variations from barcode sequencing data.
- NucHMM (Chen et al, genomics proteomics bioinformatics, 2010). A Hidden Markov Model for nucleosome positioning prediction based on DNA sequence feature.
- GenomePSD (Chen et al, Nucleic acids research. 2008). A Power Spectrum Density analysis tool for genome sequence.