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  • DANPOS (Chen et al, Genome Research, 2013): a set of 8 bioinformatics tools, including:
  1. Dpos: comparative analysis of MNase-Seq data between samples.
  2. Dpeak: comparative analysis ChIP-Seq data between samples.
  3. Dregion: analyzing broad epigenetic domains, e.g., super enhancers.
  4. Stat: statistical analysis of positions, peaks, or regions defined by DANPOS.
  5. Selector: mapping positions, peaks, or regions to any given genomic features such as genes.
  6. Profile: analyzing epigenetic signal at any given genomic regions, e.g., genes, enhancers.
  7. Wiq: a tool for genome wide quantile normalization of epigenetic data.
  8. 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.

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