Li Lab:Softwares: Difference between revisions

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


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


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


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


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


* [http://code.google.com/p/bsmap/ 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.


* [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/rseqc/ 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.


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


* [http://code.google.com/p/danpos/ 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.


* [http://code.google.com/p/bseqc/ BSeQC]: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)


* [http://code.google.com/p/cpat/ CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model]


* [http://code.google.com/p/moabs/ MOABS]: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)


* [http://code.google.com/p/bseqc/  BSeQC: Quality Control of Bisulfite Sequencing Experiments]


* [http://code.google.com/p/dychips/ DyChIPS]: An integrate solution for dynamic analysis of ChIP-sequencing


* [http://code.google.com/p/dychips/ 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.


* [http://chipexo.sourceforge.net MACE]: Model Based Analysis of [http://en.wikipedia.org/wiki/ChIP-exo ChIP-exo]


* [https://code.google.com/p/dapars/ DaPars: Dynamic analysis of Alternative PolyAdenylation? from RNA-seq]
== 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

Revision as of 22:29, 1 February 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


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
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