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Programming in R

Data Analysis in Genome Biology

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Thomas Girke

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April 19, 2018

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Outline

Some Unfinished topics

GitHub from command-line and RStudio

Running R in a terminal on local and remote systems

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Programming in R

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Some Unfinished Topics

These are some shorter topics we need to finish up:

  • Git & GitHub from command-line - URL
  • Git & GitHub from RStudio - URL
  • Running R in a terminal on local or remote systems - URL

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Outline

Some Unfinished topics

GitHub from command-line and RStudio

Running R in a terminal on local and remote systems

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Programming in R

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  • ​

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Why Programming in R?

  • Powerful statistical environment and programming language
  • Facilitates reproducible research
  • Efficient data structures make programming very easy
  • Ease of implementing custom functions
  • Powerful graphics
  • Access to fast growing number of analysis packages
  • Most widely used language in bioinformatics
  • Is standard for data mining and biostatistical analysis
  • Technical advantages: free, open-source, available for all OSs

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Online Programming Tutorial

  • Continue here!

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References and Books

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Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, …, et al (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12: 115–121

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