Examples from the Wild 2: IPython Notebooks

NGS Analysis of ChIP-seq data using IPython Notebooks to Explore

Determining Average ChIP-seq signal over promoters with Metaseq > This example demonstrates the use of :mod:metaseq for performing a common task when analyzing ChIP-seq data: what is the average signal over transcription start sites (TSS) throughout the genome?

That looks interesting but what framework is being used to make and host this?

So what are IPython Notebooks?

Allows you to code interactively in your browser and take advantage of all the aspects of HTML and other special web features, including sharing online

These are especially useful for exploring data and developing code or developing approaches to analyzing your data.

Titus Brown’s screencast and associated notebook illustrates much of this.

I’ll show two other notebooks I have made and show them interactively.

Q: You’ve run your notebook and populated the cells, now how can you share it with colleagues? A: If you follow these steps you or anyone else you share it with can see your notebook on the web.

• Upload your notebook code to somewhere. Github or simply even as a Gist will work fine.
• Place the URL here and click ‘Go!’

Note that the notebooks shared in this form will not be interactive. You can though download them and run them locally.

The future ...

The IPython Notebooks concept goes beyond Python and now they are developing a language-agnostic version of the Notebook as the Jupyter Project project.

Back to Metaseq

The page here actually has a legend with some of the plots that describes additionally apects of the exploratory analyses done on the page Determing Average ChIP-seq signal over promoters with Metaseq.