Archive for the 'Uncategorized' Category

EP Manuscript “Highly Accessed”

Tuesday, September 20th, 2011

The final PDF of our manuscript is now available on the Genome Biology website. It’s been tagged as “highly accessed” article! From the Genome Biology website: The ‘Highly accessed’ graphic appears on journal table of contents and search results to identify those articles that have been especially highly accessed, relative to their age, and the […]

X. laevis

Saturday, July 30th, 2011

One of our users asked for the files necessary to run ExpressionPlot on Affymetrix Xenopus laevis arrays: I was surprised to learn that there is no X. laevis genome yet. I took Affymetrix’s netaffx data file and probe tables and created some ExpressionPlot-compatible files by pretending each consensus sequence (basically Affymetrix’s idea of a transcript) […]

Prototype server returns

Saturday, July 9th, 2011

The prototype server is back up and running. Point your web browsers to Please let me know if you have any problems connecting and I will do my best to solve them expeditiously. Mission Bay, San Francisco: the new (temporary) home of the ExpressionPlot prototype server

Forthcoming in Genome Biology!!!

Saturday, July 9th, 2011

Our manuscript has been accepted by Genome Biology. Thanks to everyone who has contributed to the process.

prototype down

Wednesday, June 29th, 2011

Today I shut down the prototype server, It is in the caring hands of FedEx Ground until next week when I set it up in California. Please use the URL 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 […]

Paper Revision

Friday, March 25th, 2011

This week I submitted the revision to my manuscript. Without sounding too cheesy I really think that the software improved as a result of the review process. For example, it is now possible to run DESeq as an option for calculating gene expression statistics. This package makes it possible to do population-based statistics. Revised manuscript: […]

Columbia Medical School and Annotation Factory

Friday, March 25th, 2011

Just got back from a really fun trip to New York City. I visited my colleagues in the Maniatis Lab at Columbia medical school. I got a chance to work with Sean O’Keeffe who is running ExpressionPlot there. He has set up gbrowse for some of the data over there. It it a fantastic user […]

iDEA Challenge 2011: Illumina’s Data Excellence Award

Tuesday, March 15th, 2011

Illumina is holding a data visualization contest to promote the development of new ideas for visualizing high throughput sequencing data. I think ExpressionPlot fits the bill well since it makes it easy for all biologists to create the types of plots necessary for interpreting their RNA-Seq data and comparing it with other data sets.

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