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R Bloggers
Date(s): - May 28, 2015

This workshop will provide hands on experience with working hierarchical data formats (HDF5) in R.

Goals / Objectives

After completing this workshop, you will be able to:
  1. Describe what the Hierarchical Data Format (HDF5) is.
  2. Create and read from HDF5 files in R.
  3. Read and visualization time series data stored in an HDF5 format.

Before the Workshop Please

Data to Download

Install R Libraries

  • rhdf5: source("") biocLite("rhdf5")
  • ggplot2: A great plotting library. install.packages("ggplot2")
  • dplyr: data manipulation at its finest! install.packages("dplyr")
  • scales: this library makes it easier to plot time series data. install.packages("scales")

Review These Materials


Time Topic  
11:30 DPLYR Basics  
12:30 Hierarchical Data Formats - What is HDF5?  
12:30 HDFView: Exploring HDF5 Files in the Free HDFview Tool  
12:45 Introduction to HDF5 Files in R  
2:00 Working With Time Series Data Within a Nested HDF5 File in R  


To participate in the workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of the workshop.


Hierarchical Data Format 5 (HDF5) is a file format used to store, package, and simultaneously organize large quantities of related data. Although we will use R to analyze data stored in this format, HDFView is free-ware that allows for quick and easy viewing and editing of these files.


R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we recommend, RStudio, an interactive development environment (IDE).