The Bioconductor Project

Introduction to Bioconductor in R

James Chapman

Curriculum Manager, DataCamp

Bioconductor

Bioconductor

1 Bioconductor (www.bioconductor.org)
Introduction to Bioconductor in R

What do we measure and why?

  • Structure: elements, regions, size, order, relationships

structure-parts

  • Function: expression, levels, regulation, phenotypes

function

Introduction to Bioconductor in R

How to install Bioconductor packages?

  • Bioconductor has its own repository and way to install packages
# Install BiocManager
install.packages("BiocManager")

# Install the GenomicRanges package
BiocManager::install("GenomicRanges")
Introduction to Bioconductor in R

Bioconductor version and package version

# Load BiocManager
library(BiocManager)


# Check Bioconductor version
version()
Introduction to Bioconductor in R

Checking package versions

# Load GenomicRanges
library(GenomicRanges)


# Check versions for reproducibility
sessionInfo()
Introduction to Bioconductor in R

Package updates

# Check for package updates
valid()
Introduction to Bioconductor in R

Let's practice!

Introduction to Bioconductor in R

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