Analysis and Visualization of RNA-Seq Expression Data Using RStudio, Bioconductor, and Integrated Genome Browser

  • Ann E. LoraineEmail author
  • Ivory Clabaugh Blakley
  • Sridharan Jagadeesan
  • Jeff Harper
  • Gad Miller
  • Nurit Firon
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)


Sequencing costs are falling, but the cost of data analysis remains high, often because unforeseen problems arise, such as insufficient depth of sequencing or batch effects. Experimenting with data analysis methods during the planning phase of an experiment can reveal unanticipated problems and build valuable bioinformatics expertise in the organism or process being studied. This protocol describes using R Markdown and RStudio, user-friendly tools for statistical analysis and reproducible research in bioinformatics, to analyze and document the analysis of an example RNA-Seq data set from tomato pollen undergoing chronic heat stress. Also, we show how to use Integrated Genome Browser to visualize read coverage graphs for differentially expressed genes. Applying the protocol described here and using the provided data sets represent a useful first step toward building RNA-Seq data analysis expertise in a research group.

Key words

Integrated genome browser Tomato Pollen Visualization RNA-Seq Differential gene expression edgeR 



The example data set was from the Workshop in Next-Generation Sequencing (WiNGS), which was co-sponsored by the NSF Research Coordination Network on Integrative Pollen Biology (award 0955431), the NSF Plant Genome Research Program (award 1238051), and the Department of Bioinformatics and Genomics at UNC Charlotte. NIH R01 grant number 21737838 supports development of the IGB software.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Ann E. Loraine
    • 1
    Email author
  • Ivory Clabaugh Blakley
    • 1
  • Sridharan Jagadeesan
    • 2
  • Jeff Harper
    • 3
  • Gad Miller
    • 4
  • Nurit Firon
    • 2
  1. 1.Department of Bioinformatics and GenomicsUniversity of North Carolina at CharlotteCharlotteUSA
  2. 2.Department of Vegetable Research, Institute of Plant Sciences, The Volcani CenterAgricultural Research OrganizationBet DaganIsrael
  3. 3.Department of Biochemistry and Molecular BiologyUniversity of NevadaRenoUSA
  4. 4.The Mina and Everard Goodman Faculty of Life SciencesBar-Ilan UniversityRamat-GanIsrael

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