My R scripts

Microarray Analysis

This pipeline uses the EMA package as its primary workflow, together with the rgl package for creating dynamic PCA plot. Three statistical testing methods were used: T-test, SAM and LPE

  • EMA for QC and statistical tests
  • rgl for dynamic PCA plot
  • annaffy for annotation

ChIP-seq Analysis

We adapted the workflow from Zhang paper. We used bowtie2 to map the read and MACS to do peak calling. The differential binding analysis was performed using the DBChIP R package. Peak annotation was performed using the ChIPseeker package.

RNAseq Analysis

We adapted the workflow from Thomas Girke at UC Riverside. The original presentation file can be found here.

RNAseq Analysis

We adapted the workflow from Thomas Girke at UC Riverside. The original presentation file can be found here.

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Microarray Analysis



This pipeline uses the EMA package as its primary workflow, together with the rgl package for creating dynamic PCA plot. Three statistical testing methods were used: T-test, SAM and LPE

  • EMA for QC and statistical tests
  • rgl for dynamic PCA plot
  • annaffy for annotation
Stacks Image 675

ChIP-seq Analysis



We adapted the workflow from Zhang paper. We used bowtie2 to map the read and MACS to do peak calling. The differential binding analysis was performed using the DBChIP R package. Peak annotation was performed using the ChIPseeker package.

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RNA-seq gene level Analysis



We adapted the workflow from Thomas Girke at UC Riverside. The original presentation file can be found here.

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RNA-seq isoform level Analysis



My Favorite R websites

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R is a free statistical and graphical software environment I use everyday for my data analysis need. It is platform independent and many thousands of plug-in make it a very powerful data analysis option. Check it out

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As Next Generation Sequencing enters the biological research, we are counting on the power of the public to find answers to many question concerning NGS. Whatever your worried, I bet you can find a solutes here.

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Bioconductor is a R library repository for genomic and proteomic data analysis. This is a one stop shop if you need to find a method to analyze your high-throughput biological dataset. Check it out.

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RStudio is a free (for academic) IDE (Integrated Development Environemnt) for R programming. It is the best R IDE in the market

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inside-R is a comprehensive website for many R resources, including R Packages and How To ...

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Quick-R is my favorite site to find help for R code and graphic. It also has many useful links if you want to find more R information. Check it out.

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UC Riverside offer a one stop shop for all you need to know about NGS analysis with R and Bioconductor

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RDocumentation is a web service that allow users to search the verse documentation about R usages

Command Line Programming

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Home Brew



The missing package manager for OSX