Li Lab:Softwares

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(Transcriptomics)
 
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*[http://chip.dfci.harvard.edu/~wli/MAT/ Model-based Analysis of Tiling-array (MAT)]
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== Epigenomics ==
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A model-based algorithm for finding enriched regions in ChIP-Chip experiments
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*[http://chip.dfci.harvard.edu/~wli/MAT/ MAT]: Model-based Analysis of Tiling-array (PNAS 2006)
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*[http://ceas.cbi.pku.edu.cn/ Cis-regulatory Element Annotation System (CEAS)]
 
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An integrated webserver for analyzing ChIP-chip data
 
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*[http://ceas.cbi.pku.edu.cn/ CEAS]: Cis-regulatory Element Annotation System (Nucleic Acids Res 2006)
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* [http://chip.dfci.harvard.edu/~wli/xMAN/ extreme MApping of OligoNucleotides (xMAN)]
 
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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
 
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* [http://liulab.dfci.harvard.edu/MACS/ MACS]: Model-based Analysis of ChIP-sequencing (Genome Biology 2008)
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* [http://liulab.dfci.harvard.edu/MACS/ Model-based Analysis of ChIP-sequencing (MACS)]
 
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A model-based algorithm for finding enriched regions in ChIP-Seq experiments.
 
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* [http://code.google.com/p/bsmap/ BSMAP/RRBSmap]: Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)
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* [http://code.google.com/p/bsmap/ BSMAP: whole genome Bisulfite Sequence MAPping program]
 
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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.
 
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* [http://code.google.com/p/danpos/ DANPOS]: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)
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* [http://code.google.com/p/rseqc/ RSeQC: Quality Control of RNA-seq experiments]
 
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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.
 
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* [http://code.google.com/p/bseqc/ BSeQC]: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)
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* [http://code.google.com/p/danpos/ DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing]
 
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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.
 
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* [http://code.google.com/p/moabs/ MOABS]: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)
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* [http://code.google.com/p/cpat/ CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model]
 
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* [http://code.google.com/p/dychips/ DyChIPS]: An integrate solution for dynamic analysis of ChIP-sequencing
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* [http://code.google.com/p/msuite/ BSMEAT: whole genome Bisulfite Sequencing based dna MEthylatino Analysis Tools]
 
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* [http://chipexo.sourceforge.net MACE]: Model Based Analysis of [http://en.wikipedia.org/wiki/ChIP-exo ChIP-exo] (Nucleic Acids Res 2014)
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* [http://code.google.com/p/dychips/ DyChIPS: An integrate solution for dynamic analysis of ChIP-sequencing]  
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== Transcriptomics ==
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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.
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* [http://code.google.com/p/rseqc/ RSeQC]: Quality Control of RNA-seq experiments (Bioinformatics 2012)
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* [http://code.google.com/p/cpat/ CPAT]: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model (Nucleic Acids Res 2013)
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* [https://code.google.com/p/dapars/ DaPars]: Dynamic analysis of Alternative PolyAdenylation from RNA-seq (Nature 2014; Nature Communications 2015)

Current revision

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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)
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