Introduction and setup

Introduction to Bioconductor

Figure 1

Timeline of major Bioconductor milestones alongside technological advancements.

Figure 2

Timeline of release dates for selected Bioconductor and R versions.

Figure 3

Sequencing Ecosystem.

Installing Bioconductor packages

Figure 1

The package BiocManager is available from the CRAN repository and used to install packages from the Bioconductor repository.

Figure 2

Timeline of release dates for selected Bioconductor and R versions.

Getting help

Figure 1

The Bioconductor support site.

S4 classes in Bioconductor

Figure 1

S4 classes, generics, and methods.

Figure 2

Metadata columns.

Figure 3

Run-length encoding.

Working with biological sequences

Working with genomics ranges

Figure 1

Example uses of the GenomicRanges algebra.

Figure 2

Example of intervals.

Figure 3

Example of genomic intervals.

Working with annotations

The SummarizedExperiment class

Figure 1

Schematic representation of the SummarizedExperiment class.