Welcome to Rgenetics@Lazarus_Lab

Recent Bloggery

• functional test enhancements for Galaxy continued  -- Posted on 2009-12-06 16:14 : author rerla
• functional test enhancements for Galaxy  -- Posted on 2009-11-30 14:39 : author rerla : categories functional_tests galaxy bitbucket
• Some R dependencies on ubuntu (moved - old from june 2009)  -- Posted on 2009-11-19 14:56 : author rerla
• Travails trying to get the WTCCC data  -- Posted on 2009-11-18 18:22 : author rerla
• Testing shellfish with hapmap3 data  -- Posted on 2009-11-18 04:25 : author rerla : categories shellfish eigenPCA ancestry rgenetics
• Notes on Galaxy clustering setup as at November 2009  -- Posted on 2009-11-16 04:08 : author rerla : categories clustering galaxy
• Shellfish for Ancestry PCA  -- Posted on 2009-11-15 17:24 : author rerla : categories shellfish eigenPCA ancestry rgenetics
• Hardware failure, november 2009: lessons  -- Posted on 2009-11-12 23:26 : author rerla : categories hardware disaster_recovery
• Galaxy, R and Xvfb  -- Posted on 2008-09-13 21:34 : author rerla : categories R framebuffer X11
• Three demonstration expression tools now working  -- Posted on 2008-09-07 22:50 : author rerla

Useful links

 Rgalaxy Development site

Rgalaxy screencasts and demonstrations - unstable!

 Galaxy Wiki, Documentation, screencasts and source

 Main Galaxy instance

 Galaxy TEST site for Rgenetics Tools - development tools only

Other Lazarus_Lab activities:  ESP Electronic Support for Public Health

(The old Rgenetics development site is archived here)

Olds

November 2009	October 2009	April 2009	February 2009	Older news
Backups recovered to new hardware after ugly hardware meltdown	http://test.g2.bx.psu.edu Rgenetics on the Galaxy TEST instance	Some design notes for a new project	Competitive renewal due for review June 4th	News Archives

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

Odds and Ends

Galaxy Ubuntu Jeos vmbuilder wrapper  Channing Infrastructure

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.