Intro to R and Bioconductor

Intro to R and Bioconductor

Keywords

Prerequisite, R-programming

Authors

  • Jenny Drnevich @jenny

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Description

R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data.

Aims

This module aims to take the novice and turn them into a beginning R user. We will describe the R environment and programming language structure so they can start to read and write code and know where to get additional help. The Bioconductor project will be described in general.

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Prerequisites

  • Basic computer literacy (point-and-click interface)

Target audience

  • Graduates students/post docs/beginning faculty with an interest in learning R, particularly for genomic data analysis. No experience with R or other programming languages are required.

Learning objectives

  • Be able to describe what R is and how the programming environment works.
  • Be able to download and install R and add-on packages
  • Be able to read, understand and write simple R code
  • Appreciate how R can be used to analyze various types of scientific data, particularly genomic data using packages from Bioconductor.

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Materials

  • Lecture
  • R Installation and Use Guide
  • R swirl instructions
  • Practice codes
  • Understanding R code cheat sheet

Data

  • Practice R objects

Description

Small collection of R data objects used in the practice questions at the end of the practice codes. Origin unimportant; used to illustrate manipulation of different object types.

Availability

  • Practice R objects

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Technical requirements

R version >= 3.0

Literature references

  • Programming tools: Adventures with R
  • Orchestrating high-throughput genomic analysis with Bioconductor

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Keywords: Prerequisite, R-programming

Authors: Jenny Drnevich @jenny

External resources:
Intro to R and Bioconductor https://tess.elixir-europe.org/materials/intro-to-r-and-bioconductor R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data. Prerequisite, R-programming