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Overview

In this lab, we'll look at how to use cummeRbund to visualize our gene expression results from cuffdiff.  CummeRbund is part of the tuxedo pipeline and it is an R package that is capable of plotting the results generated by cuffdiff.

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Figure from: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell et al, Nature Protocols, 2013. 

Introduction

CummeRbund is powerful package with many different functions. Cuffdiff produces a lot of output files and all the output files are related by sets by IDs.

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•   readCufflinks- Most important function designed to read all the output files that cuffdiff generates into an R data object (of class CuffSet).
  •  cuff_data <- readCufflinks(diff_out)
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  • CummeRbund has at least 6 classes that it will place different parts of your data in.
  • Now you can access information using different functions:  gene information using genes(cuff_data), your isoform level output using isoforms(cuff_data), TSS related groups using tss(cuff_data) and so forth
    
    

What can you do with cummeRbund?

• Global statistics on data for quality, dispersion, distribution of gene expression scores etc.
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• Plot things for specific features or genes

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Figures from http://compbio.mit.edu/cummeRbund/manual_2_0.html

Get your data

MAKE SURE YOU ARE IN THE IDEV SESSION FOR THIS!

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pdf(file="rala.pdf")
mygene2 <- getGene(cuff_data, 'Rala')
expressionBarplot(mygene2)
expressionBarplot(isoforms(mygene2))
dev.off()

Take cummeRbund for a spin...

CummeRbund is powerful package with many different functions. Above was an illustration of a few of them. Try any of the suggested exercises below to further explore the differential expression results with different cummeRbund functions.

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