Li Lab:Softwares: Difference between revisions

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* Whole Genome Phylogeny
== Epigenomics ==
Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis
 
*[http://chip.dfci.harvard.edu/~wli/MAT/ MAT]: Model-based Analysis of Tiling-array (PNAS 2006)
 
 
*[http://ceas.cbi.pku.edu.cn/ CEAS]: Cis-regulatory Element Annotation System (Nucleic Acids Res 2006)
 
 
* [http://liulab.dfci.harvard.edu/MACS/ MACS]: Model-based Analysis of ChIP-sequencing (Genome Biology 2008)
 
 
* [http://code.google.com/p/bsmap/ BSMAP/RRBSmap]: Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)
 
 
* [http://code.google.com/p/danpos/ DANPOS]: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)
 
 
* [http://code.google.com/p/bseqc/ BSeQC]: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)




*[http://genome.dfci.harvard.edu/~xsliu/HMMTiling/ HMMTiling]
* [http://code.google.com/p/moabs/ MOABS]: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)
A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays




*[http://chip.dfci.harvard.edu/~wli/MAT/ Model-based Analysis of Tiling-array (MAT)]
* [http://code.google.com/p/dychips/ DyChIPS]: An integrate solution for dynamic analysis of ChIP-sequencing
A model-based algorithm for finding enriched regions in ChIP-Chip experiments




*[http://ceas.cbi.pku.edu.cn/ Cis-regulatory Element Annotation System (CEAS)]
* [http://chipexo.sourceforge.net MACE]: Model Based Analysis of [http://en.wikipedia.org/wiki/ChIP-exo ChIP-exo] (Nucleic Acids Res 2014)
An integrated webserver for analyzing ChIP-chip data


== Transcriptomics ==


* [http://chip.dfci.harvard.edu/~wli/xMAN/ extreme MApping of OligoNucleotides (xMAN)]
* [http://code.google.com/p/rseqc/ RSeQC]: Quality Control of RNA-seq experiments (Bioinformatics 2012)
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




* [http://liulab.dfci.harvard.edu/MACS/ Model-based Analysis of ChIP-sequencing (MACS)]
* [http://code.google.com/p/cpat/ CPAT]: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model (Nucleic Acids Res 2013)
A model-based algorithm for finding enriched regions in ChIP-Seq experiments.




BSMAP: Bisulfite Sequence Mapping
* [https://code.google.com/p/dapars/ DaPars]: Dynamic analysis of Alternative PolyAdenylation from RNA-seq (Nature 2014; Nature Communications 2015)
coming soon..

Latest revision as of 11:41, 28 September 2014

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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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