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Epigenomics

  • MAT: Model-based Analysis of Tiling-array (PNAS 2006)


  • CEAS: Cis-regulatory Element Annotation System (Nucleic Acids Res 2006)


  • MACS: Model-based Analysis of ChIP-sequencing (Genome Biology 2008)


  • BSMAP/RRBSmap: Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)


  • DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)


  • BSeQC: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)


  • MOABS: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)


  • DyChIPS: An integrate solution for dynamic analysis of ChIP-sequencing


  • MACE: Model Based Analysis of ChIP-exo (Nucleic Acids Res 2014)

Transcriptomics

  • RSeQC: Quality Control of RNA-seq experiments (Bioinformatics 2012)


  • CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model (Nucleic Acids Res 2013)


  • DaPars: Dynamic analysis of Alternative PolyAdenylation from RNA-seq (Nature 2014; Nature Communications 2015)