I get a lot of requests in the core about running a "pathway analysis." Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq,...
I direct the Bioinformatics Core at the University of Virginia, and I'm hiring. Visit this link on the UVA Jobs website for more information. Here's the description: The University of Virginia Bioinformatics Core is seeking a full-time position as a b...
Kevin White from the University of Chicago will be giving a special guest lecture at NCI next week on systems biology approaches to mine genomics data for biomarkers and therapeutic targets. The lecture will be available online as a videocast. Title...
Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of di...
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 no...
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,...
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 experim...
BioMart recently got a facelift. I'm not sure if this was always available in the old BioMart, but there's now a link to a gene ID converter that worked pretty well for me for converting S. cerevisiae gene IDs to standard gene names. It looks like the ...
Gene Expression Omnibus is NCBI's repository for publicly available gene expression data with thousands of datasets having over 600,000 samples with array or sequencing data. You can download data from GEO using FTP, or download and load the data direc...
