Li Lab:Softwares

Home        People        Publications        Collaborations        Software        Positions        Contact       

• 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

• extreme MApping of OligoNucleotides (xMAN)

A intuitive and efficient algorithm for the mapping of millions of query oligonucleotide fragments to the genome of any given length, at least an order of magnitude faster than other popular existing tools

• 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

• BSMEAT: whole genome Bisulfite Sequencing based dna MEthylatino Analysis Tools

• 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.