Thursday, December 15, 2011

Query a MySQL Database from R using RMySQL

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame.

Galaxy Project Group on CiteULike and Mendeley

The Galaxy Project started using CiteULike to organize papers that are about, use, or reference Galaxy. The Galaxy CiteULike group is open to any CUL user, and once you join, you can add papers to the group, assign tags, and rate papers.

While not a CUL user, I'm a big fan of Mendeley for managing references, PDFs, and creating bibliographies (and so are many of you). I'm happy to hear that the Galaxy folks also set up a Galaxy Mendeley Group, also open to the public for anyone to join.  If you join the Galaxy public Mendeley group, all of the groups references will show up in your Mendeley library (and these won't count against your personal quota).

Just one important thing to note: The Mendeley group is a mirror of the CiteULike group, so if you want to add more publications to the Galaxy Group, add them on CiteULike, not Mendeley (it doesn't work the other way around - papers added to Mendeley won't make it to the CUL group).

Galaxy Project Group on CiteULike and Mendeley

Thursday, December 8, 2011

RNA-Seq & ChiP-Seq Data Analysis Course at EBI

I just got this announcement from EMBL-EBI about an RNA-seq/ChIP-seq analysis hands-on course. Find the full details, schedule, and speaker list here.

Title: Advanced RNA-Seq and Chip-Seq Data Analysis Course
Date: May 1-4 2012
Venue: EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK
Registration Closing Date: March 6 2012 (12:00 midday GMT)

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research. The aim of this course is to familiarize the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches.

Lectures will give insight into how biological knowledge can be generated from RNA-seq and ChIP-seq experiments and illustrate different ways of analyzing such data Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq and ChIP-seq data under the guidance of the lecturers and teaching assistants. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.

The course covers data analysis of RNA-Seq and ChIP-Seq experiments.
Topics will include: alignment, data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.

Tuesday, December 6, 2011

An example RNA-Seq Quality Control and Analysis Workflow

I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experiments using the FastX toolkit and FastQC.

The second set (PDF)  gives an example RNA-seq workflow using TopHat, SAMtools, Python/HTseq, and R/DEseq.

If you're doing any RNA-seq work these are both really nice resources to help you get a command-line based analysis workflow up and running (if you're not using Galaxy for RNA-seq).

Monday, December 5, 2011

Webinar: Applications of Next-Generation Sequencing in Clinical Care

I just got an email from Illumina about a webinar that looks interesting this Wednesday at 9am PST (noon EST) on clinical applications of next-gen sequencing.

Date: Wednesday, December 7, 2011
Time: 9:00 AM (PST)
Speaker: Rick Dewey, MD, Stanford Center for Inherited Cardiovascular Disease

Next-generation sequencing (NGS) presents both challenges and opportunities for clinical care. Dr. Dewey will share examples from his experience at Stanford, successful and otherwise, in which NGS has been applied to cases of familial cardiomyopathy, and other inherited conditions. Bring your questions for a Q&A session. In this webinar, Dr. Dewey will discuss approaches to: Data storage and management; Error identification and reduction; Disease risk encoded in the reference sequence; and Variant validation.

The webinar will be recorded and available to you afterwards if you register.

Registration - Applications of Next-Generation Sequencing in Clinical Care
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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.