Tag Archives: R Genetics

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

R Genetics is back up

The other day I did a post about the UCSC, Galaxy, and R Genetics presentations at ASHG.  At the time, though, I couldn’t get to R Genetics at the regular url (http://www.rgenetics.org).  I contacted Ross Lazarus and found out there had been a server meltdown over the weekend.

Well, I have just received word that the materials are back up, and/or in the process of being restored.  You can access the URL above to get to the Lazarus projects site, or for going directly to the R Genetics tools in Galaxy go to this site: http://rgenetics.org/trac/rgalaxy.  At this time there is still a warning that some files are still awaiting recovery.  And if you find anything is missing do holler.

From the Rgenetics Galaxy tools site you can access the test server at Galaxy, where the R Genetics tools are in beta. From that page click the bullet name:

The interface looks similar to the regular Galaxy, but look down the list to find these:
rgenetics_galaxy

We did a training a few months back where the workshop folks expressed much interest in having Galaxy be the interface for R. And it’s on the way….

EDIT: I have to close comments on this post because some Russian spammer has locked on to it and keeps clogging up the spam filter….

UCSC, Galaxy, and R Genetics at ASHG

Folks from UCSC Genome Browser, Galaxy, and the R Genetics project* gave workshops at the recent ASHG meeting.  They were very well attended–in fact, I heard they were the first things to sell out after the luau!  And the attendees I spoke with told me they were pleased with the opportunity to hear from these teams. At our booth other people were hoping to get some materials because they couldn’t attend either because the missed out on the sign up or had other stuff concurrently.  So I thought I’d do a quick post on what was covered.

This year there were two sessions, a more introductory level and then a more advanced level.  But there was still a lot of overlap between the groups, many people attended both sessions.

Bob Kuhn from UCSC presented features of the UCSC Genome Browser using a clinical report as a jumping-off point.  It’s a great idea, and people have been asking us for that kind of case study perspective as well.  If you’d like to see his workshop materials and the steps he was taking people through, check out this page: UCSC Genome Browser Workshop at ASHG 2009.

Anton Nekrutenko provided nice examples of analyses that can be performed with Galaxy that would be of interest to the ASHG folks.  Ross Lazarus demonstrated some tools from the R Genetics project, with a preview of their implementation in Galaxy.  This is a very nice direction, as people are always asking us for better web interfaces for some of these types of tools.

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If you wanted to get up to speed on these tools you could check out our training materials on UCSC Genome Browser and Galaxy.  Both of those teams sponsor us to provide these tutorials for free and you can check them out on our site:

UCSC Genome Browser (3 tutorials at this time): Introduction, Advanced, Additional  Tools.

Galaxy: Introduction

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*Update: server issues at the R Genetics link right now are causing problems so I’m taking it off for now.  It may have to move, and when I have an update I’ll re-link or get you the new spot.