Archive for June, 2011

prototype down

Wednesday, June 29th, 2011

Today I shut down the prototype server, als-research.mit.edu. It is in the caring hands of FedEx Ground until next week when I set it up in California. Please use the URL als-research.expressionplot.com from now on.

Canonical Distribution Tool

Friday, June 10th, 2011

Just finished creating a new tool for quality control. It is available starting in EP version 1.6. I am calling it the “canonical distribution” tool, because it analyzes the positional distribution of reads near genomic landmarks (such as splice sites, start/stop codons etc) of the UCSC “canonical” transcripts. Here’s an example: Using this tool requires […]

Manuscript Revision 2

Friday, June 3rd, 2011

Finished revision 2 of the paper last week. The associated version of ExpressionPlot is 1.3. There are several improvements over the previous revision. Limma is now used to calculate differential expression statistics for microarrays. User-defined event types are now available through the event_types.tsv interface (described in User’s Guide) Annotation pipeline is now part of ExpressionPlot […]

A web-based framework for analysis of RNA-Seq and microarray gene expression data