Analysis

Epigenomics
450k Chip Analysis Methylation Pipeline

The ChAMP package is designed for the analysis of Illumina Methylation beadarray data (EPIC and 450k) and provides a pipeline that integrates currently available 450k and EPIC analysis methods. The new version of ChAMP, extends and improves this analysis pipeline, adding novel and enhanced functionalities, including detection of differentially methylated genomic blocks (DMB), Gene Set Enrichment Analysis (GSEA), a variety of methods for correcting cell-type heterogeneity and detection of differentially methylated gene modules. Notably, the new package provides a series of web-based graphical user interfaces (GUIs), which facilitate analyses and enhance user-experience.

Population Genomics
MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures.

MultiWaver series software was designed to infer population admixture history in case of various and complex scenarios. The earlier version of MultiWaver considered only the discrete admixture models. In the newly developed version MultiWaver 2.0, we implemented a more flexible framework to automatically select an optimal admixture model among discrete models and continuous models.

AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals.

AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals in a way to save space with a rounded and nice-looking graph. It requires Perl and R software to run the program. It is user-friendly and many details in the graph could be handled with command lines (Please check the Manual for detailed information).

iMAAPs is a powerful tool to estimate multiple-wave population admixed time, which is currently designed to infer the two-way, multiple-wave admixture based on admixture induced LD.

iMAAPs is a powerful tool to estimate multiple-wave population admixed time, which is currently designed to infer the two-way, multiple-wave admixture based on admixture induced LD. This software can deal with genotype data, haplotype data and the data re-coded according to admixture ancestries.

AdmixInfer is designed to optimize the parameters of admixture model via maximum likelihood estimation and figure out the model best fit the data.

AdmixInfer is designed to optimize the parameters of admixture model via maximum likelihood estimation and figure out the model best fit the data. The optimization is under assumption of HI (Hybrid Isolation), GA(Gradual Admixture), CGFR (Continuous Gene Flow Recipient) and CGFD (Continuous Gene Flow Donor) model.

WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.

WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.

SC (Spatial Coalescent simulator) is a computer simulation tool for modeling spatial coalescent with recombination process.

SC (Spatial Coalescent simulator) is a computer simulation tool for modeling spatial coalescent with recombination process. The algorithm implemented in SC is an improvement of the Wiuf and Hein algorithm (Wiuf and Hein, 1999). SC is proven to be the only precise ancestral recombination graph (ARG) simulator (Wiuf and Hein’s has some redundant and MaCS misses some information) such as the distribution of ARG generated by SC is identical to that generated by a typical back-in-time model adopted by ms. SC is developed based on Macs-0.4e, all macs options are not changed. 

Epitranscriptomics
RNA-editing Analysis-pipeline to Decode All twelve-types of RNA-editing events

A pipeline to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.

Transcriptomics
A combined strategy to identify junction reads from back spliced exons and intron lariats.

A combined strategy to identify circular RNAs (circRNAs and cIRNAs).

A circular RNA analysis toolset

A toolset for circular RNA Identification and characterization.

Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq (CLEAR/CIRCexplorer3)

A toolset for circular RNA identification, characterization and expression analysis.