Bioconductor open source software for bioinformatics

Web Page: http://www.bioconductor.org/developers/gsoc2013/

Mailing List: mailto:gsoc-bioc@lists.fhcrc.org

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, >670 software packages, and an active user community. Goals of the Bioconductor project include but are not limited to: 1 Supporting a community of many thousands of computational biologists in their efforts to explore rapidly changing and growing data. 2 Enabling this community to avoid reinventing the wheel by providing a mechanism to extend each others existing inventions. 3 Maintaining a standard set of core objects, packages and annotations for building these shared tools. 4 Promoting reproducible research by maintaining a common codebase for computational biology and mechanisms for sharing that code within the wider community.

Projects

• Application for Project 3: BiocParallel / BatchJobs integration Application for Bioconductor Project 3: "BiocParallel / BatchJobs integration" as proposed on the Bioconductor web site (http://www.bioconductor.org/developers/gsoc2013/)
• Shiny Bioconductor Objects Project The Shiny package allows for easy creation of interactive web graphics from R objects. Bioconductor packages have many objects that represent biological data or results. For each of these Bioconductor objects, there exists a typical set of visualizations to help users explore their data. Normally, these visuals are replotted several times until certain parameters are tweaked to show the image in a way that conveys a specific insight. This project pairs these standard Bioconductor objects with more user-friendly Shiny visualizations via new display() methods.