Li Lab:Softwares

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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)