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*[http://genome.dfci.harvard.edu/~xsliu/HMMTiling/ HMMTiling]
== Epigenomics ==
A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays


*[http://chip.dfci.harvard.edu/~wli/MAT/ MAT]: Model-based Analysis of Tiling-array (PNAS 2006)


*[http://chip.dfci.harvard.edu/~wli/MAT/ Model-based Analysis of Tiling-array (MAT)]
A model-based algorithm for finding enriched regions in ChIP-Chip experiments


*[http://ceas.cbi.pku.edu.cn/ CEAS]: Cis-regulatory Element Annotation System (Nucleic Acids Res 2006)


*[http://ceas.cbi.pku.edu.cn/ Cis-regulatory Element Annotation System (CEAS)]
An integrated webserver for analyzing ChIP-chip data


* [http://liulab.dfci.harvard.edu/MACS/ MACS]: Model-based Analysis of ChIP-sequencing (Genome Biology 2008)


* [http://chip.dfci.harvard.edu/~wli/xMAN/ 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


* [http://code.google.com/p/bsmap/ BSMAP/RRBSmap]: Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)


* [http://liulab.dfci.harvard.edu/MACS/ Model-based Analysis of ChIP-sequencing (MACS)]
A model-based algorithm for finding enriched regions in ChIP-Seq experiments.


* [http://code.google.com/p/danpos/ DANPOS]: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)


* [http://code.google.com/p/bsmap/ BSMAP: whole genome Bisulfite Sequence MAPping program]  
 
Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome.  However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation. We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible. 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. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.<math>Insert formula here</math>
* [http://code.google.com/p/bseqc/ BSeQC]: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)
 
 
* [http://code.google.com/p/moabs/ MOABS]: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)
 
 
* [http://code.google.com/p/dychips/ DyChIPS]: An integrate solution for dynamic analysis of ChIP-sequencing
 
 
* [http://chipexo.sourceforge.net MACE]: Model Based Analysis of [http://en.wikipedia.org/wiki/ChIP-exo ChIP-exo] (Nucleic Acids Res 2014)
 
== Transcriptomics ==
 
* [http://code.google.com/p/rseqc/ RSeQC]: Quality Control of RNA-seq experiments (Bioinformatics 2012)
 
 
* [http://code.google.com/p/cpat/ CPAT]: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model (Nucleic Acids Res 2013)
 
 
* [https://code.google.com/p/dapars/ DaPars]: Dynamic analysis of Alternative PolyAdenylation from RNA-seq (Nature 2014; Nature Communications 2015)

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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