What is EaSeq?
EaSeq is a software environment developed for interactive exploration, visualization and analysis of genome-wide sequencing data – mainly ChIP-seq. Combined with a comprehensive toolset, we believe that this can accelerate genome-wide interpretation and understanding (More here).
EaSeq is controlled by a graphical user inferface, runs on a typical PC, and is free of charge. In EaSeq, you can quickly switch back and forth between visualizing individual genomic loci (similar to a genome browser) and thousands of loci at a time. A subset of underlying loci in a genome-wide abstraction, e.g. a scatter diagram or a clustered heatmap, can be inspected just by selecting that part of the plot. In this way, you can e.g. identify a subpopulation of CpG-islands or genes near the binding sites of a particular transcription factor and enriched in a histone mark of interest.
EaSeq contains a variety of analysis and visualization tools, such as peak-finding, quantitation, normalization, clustering, distance analysis, randomization, scoring etc., so the amount of file transfers and format conversions between different tools is reduced. Plots can be rearranged, duplicated, and with a few clicks instructed to show another population of genomic loci, so you can e.g. nimbly reuse your visualization of e.g. an imported set of transcription factor binding sites and make a similar visualization of an another set.
EaSeq automatically generates descriptions of how the data were handled, which helps you to go back and inspect how an earlier analysis was done. It can store all underlying data, your assembly of plots and these descriptions in a single compact file, which can be exchanged or reused later.
Why did we make it?
ChIP-seq and related methods have become central for many fields in biology and medicine. Ideally, exploration and analysis of such data (homemade or from consortia) should be as quick and feasible as microscopy or FACS data analysis is.
Using ChIP-seq ourselves, we found that this was not really the case… Often, bioinformatics becames a bottleneck, and testing a new hypothesis could take weeks, keeping ChIP-seq from reaching its full potential. We were missing a visual, versatile, and user-friendly tool that could help us to accelerate data exploration and interpretation – preferably also one that reduced data handling, temporary file generation, and book-keeping.
Eventually, we developed this ourselves.
After using EaSeq for hundreds of ChIP-seq datasets, we can camly state that it accelerates visualization, helps hypothesis generation, and ensures a better concordance between abstract genome-wide interpretations and underlying data at single loci. It is now time for EaSeq to help the many biologists, who cannot prioritize to become skilled programmers, in investigating and understanding their own genome-wide data.
EaSeq has become comprehensive, and an interactive graphical user interface does not eliminate the learning curve. We have integrated several means to help you getting started, such as tutorials, in the program. But suggestions on how to make EaSeq easier to use, questions, bug reports, and ideas for new features are warmly welcomed.
We hope that EaSeq will help ChIP-seq to become as feasible for you as microscopy is.
– Mads Lerdrup