rtracklayer

rtracklayer provides programmatic access to genome browsers and manipulation of genomic annotations within R to integrate experimental data with genome browser views.

Key Features:

• Annotation Transfer: Transfer annotation tracks to and from supported genome browsers, currently including UCSC.
• Browser View Manipulation: Create and manipulate browser views focused on specific genomic regions or sets of annotations.
• Format Support: Import, export, and manipulate annotation and sequence formats including GFF, BED, bedGraph, BED15, WIG, BigWig, and 2bit.
• Browser State Control: Query and modify browser state, including adjusting the current viewport.
• Extensibility in R: Provide an extensible framework within the R programming environment for integrating analysis and browser interactions.

Scientific Applications:

• Visualization of large-scale genomic data: Display and examine annotation tracks and continuous data across genomic regions for interpretation of experimental results.
• Integration with R-based analyses: Combine genome browser views with R workflows to link computational analyses and visual representations.
• Targeted regional studies: Focus analyses on specific genomic regions or annotation subsets for hypothesis-driven investigation.
• Multi-format data workflows: Exchange and harmonize data across GFF, BED, bedGraph, BED15, WIG, BigWig, and 2bit formats within analysis pipelines.

Methodology:

Leverages the extensibility of the R programming environment to interact with genome browsers and allows querying and modification of browser state, such as adjusting the viewport.