Welcome to Rgenetics@Lazarus_Lab

Other Lazarus_Lab activities: Channing Infrastructure, ESP and Anton Nekrutenko's Galaxy project

(The old Rgenetics development site is archived here)

News

April 2009	February 2009	Older news
Some design notes for a new project	Competitive renewal due for review June 4th	News Archives

Useful links

Rgalaxy Development site

Rgalaxy screencasts and demonstrations

Galaxy Wiki, Documentation, screencasts and source

Main Galaxy instance

Test Galaxy(Rgalaxy tools are available)

Rgenetics Project Summary

The Rgalaxy rgenetics and Rexpression toolkits for Galaxy are designed to provide biologists with easy access to a wide and growing range of popular third-party tools such as Plink for handling whole genome genotype and and Bioconductor for gene expression data. This access is through a deceptively simple looking web interface, provided by the Galaxy framework, which supports persistent, shareable workspaces where all steps are recorded, and transparent access to popular third party data repositories such as UCSC and GEO. The Rgalaxy tools hide most of the ugly complexities of working with heterogeneous data layout and command format syntax and semantics from the biologist, and requires little training for most users.

Some Technical notes

Technical notes here including some notes on datatypes and installing a local mirror

The first products of this project, the rgenetics tools in BioConductor, are packaged for interactive use in R and distributed through the normal BioConductor channels. The Galaxy versions of the tools are currently available for testing here, or at the test Galaxy site. If you want your own private copy, you need to follow the instructions below. The rgalaxy data types are now in the main Galaxy trunk distribution. A large number of external packages are also needed to make full use of the rgenetics tools but an svn checkout will give you a flying start after you adjust your tool_conf.xml file appropriately based on the samples in the svn.

All of the software we use (including this Trac/Subversion site) and produce is licensed under an approved open source license.

Support

Work available here is supported by NIH RO1HG003646 “A Genetic Association Research Statistical Framework” - Ross Lazarus is the PI

trac (this website) docs

• TracGuide -- Built-in Documentation
• The Trac project -- Trac Open Source Project
• Trac FAQ -- Frequently Asked Questions
• TracSupport -- Trac Support

For a complete list of local wiki pages, see TitleIndex.