Li Lab:Softwares

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• Model-based Analysis of Tiling-array (MAT)

A model-based algorithm for finding enriched regions in ChIP-Chip experiments

• Cis-regulatory Element Annotation System (CEAS)

An integrated webserver for analyzing ChIP-chip data

• Model-based Analysis of ChIP-sequencing (MACS)

A model-based algorithm for finding enriched regions in ChIP-Seq experiments.

• BSMAP: whole genome Bisulfite Sequence MAPping program

BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage.

• RSeQC: Quality Control of RNA-seq experiments

RseQC comprehensively evaluatse different aspects of RNA-seq experiments, such as sequence quality, GC bias, PCR bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity, and read distribution over the genome structure.

• DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS is specifically developed for comparison between nucleosome maps generated based on high-throughput sequencing, it detects changes in nucleosome position, occupancy, or fuzziness at single nucleotide resolution.

• CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model

• BSeQC: Quality Control of Bisulfite Sequencing Experiments

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

DyChIPS is designed for comparative analysis of ChIPSeq data whose targets tend to be broad and are widely distributed across the genome, such as histone modification or some chromatin-binding proteins.

• DaPars: Dynamic analysis of Alternative PolyAdenylation? from RNA-seq