Li Lab:Softwares: Difference between revisions
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== Epigenomics == | |||
*[http://chip.dfci.harvard.edu/~wli/MAT/ MAT]: Model-based Analysis of Tiling-array (PNAS 2006) | *[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 | *[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 | * [http://liulab.dfci.harvard.edu/MACS/ MACS]: Model-based Analysis of ChIP-sequencing (Genome Biology 2008) | ||
* [http://code.google.com/p/bsmap/ BSMAP/RRBSmap: | * [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/ | * [http://code.google.com/p/danpos/ DANPOS]: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013) | ||
* [http://code.google.com/p/ | * [http://code.google.com/p/bseqc/ BSeQC]: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013) | ||
* [http://code.google.com/p/ | * [http://code.google.com/p/moabs/ MOABS]: MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014) | ||
* [http://code.google.com/p/ | * [http://code.google.com/p/dychips/ DyChIPS]: An integrate solution for dynamic analysis of ChIP-sequencing | ||
* [http:// | * [http://chipexo.sourceforge.net MACE]: Model Based Analysis of [http://en.wikipedia.org/wiki/ChIP-exo ChIP-exo] | ||
== Transcriptomics == | |||
* [ | * [http://code.google.com/p/rseqc/ RSeQC]: Quality Control of RNA-seq experiments (Bioinformatics 2012) | ||
* [http://code.google.com/p/ | * [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
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
