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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

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rtracklayer: an R package for interfacing with genome browsers.

Michael Lawrence¹, Robert Gentleman, Vincent Carey

¹Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA. mflawren@fhcrc.org

Bioinformatics (Oxford, England)

|May 27, 2009

Summary

The rtracklayer package enables R users to integrate experimental data with genome browsers. This tool facilitates data transfer and manipulation for focused genomic region analysis, currently supporting the UCSC genome browser.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The rtracklayer package is available from Bioconductor.
A quick-start vignette is included for user guidance.

Purpose of the Study:

To facilitate the integration of R-based experimental data analyses with existing genome browsers.
To enable users to transfer annotation tracks between R and genome browsers.
To allow manipulation of browser views for focused analysis of specific genomic regions.

Main Methods:

Utilizing the rtracklayer package in R for data integration.
Implementing functions for transferring annotation tracks.
Developing methods for creating and manipulating genome browser views.

Main Results:

The rtracklayer package successfully integrates R analyses with genome browsers.
Users can transfer annotation data to and from genome browsers.
Browser views can be customized to focus on specific genomic annotations.

Conclusions:

The rtracklayer package enhances R's utility in genomics by bridging experimental data analysis with visualization.
It supports seamless data exchange and focused exploration of genomic data within browsers.
Current implementation supports the UCSC genome browser, with potential for future expansion.