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Signed-off-by: vsoch <vsochat@stanford.edu>
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vsoch committed Oct 6, 2020
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---
layout: post
title: "ideogram.js"
title: "Ideogram.js"
date: 2020-10-04 08:30:46
author: "@vsoch"
annotate_criteria: https://rseng.github.io/software/repository/github/eweitz/ideogram/annotate-criteria/
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Visualization is a powerful tool to understand and explore data, but it's often overlooked.
In scientific visualization, the best libraries can allow a scientist to bring life to something that we
otherwise might not be able to see. Thus, for the software showcase this week, we are proud to share <a href="https://github.com/eweitz/ideogram" target="_blank">ideogram.js</a>,
otherwise might not be able to see. Thus, for the software showcase this week, we are proud to share <a href="https://github.com/eweitz/ideogram" target="_blank">Ideogram.js</a>,
a visualization library in JavaScript that can draw and animate genome-wide datasets.

<br>
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<!--more-->

- [What is ideogram.js](#what-is)
- [What is Ideogram.js](#what-is)
- [How do I cite it?](#cite)
- [How do I contribute to the software survey](#contribute)
- [Where can I learn more?](#learn-more)
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[![All human genes](https://raw.githubusercontent.com/eweitz/ideogram/master/examples/vanilla/ideogram_histogram_all_human_genes.png)](https://eweitz.github.io/ideogram/annotations_histogram.html)

The lead developer, Eric Weitz, started working on Ideogram.js in [February 2015](https://github.com/eweitz/ideogram/commit/b615e0f0a06fee451f07f5b8582eb772d1097f28), and has developed it as a personal side project on nights and weekends almost daily since.

#### Why is it useful?

As a developer, it's very appealing to have a base or core library that I'm empowered to use to create custom dashboards or interfaces.
Here is an example of that [provided on the site](https://eweitz.github.io/ideogram/differential-expression) showing differential expression:
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<a id="cite">
## How do I cite it?

The software does not appear to have an associated paper or DOI, and we will open an issue to request one!
The lead developer recommends the following two citations. The first is not bibtex, but a general
reference to the repository:

```
Weitz, Eric M. Ideogram.js. 2015. https://github.com/eweitz/ideogram.
```

the second is related work that uses Ideogram.js.

```
@Article{ 10.12688/f1000research.9762.1,
AUTHOR = { Weitz, EM and Pantano, L and Zhu, J and Upton, B and Busby, B},
TITLE = {Viewing RNA-seq data on the entire human genome [version 1; peer review: 3 approved]
},
JOURNAL = {F1000Research},
VOLUME = {6},
YEAR = {2017},
NUMBER = {596},
DOI = {10.12688/f1000research.9762.1}
}
```

You can view the paper [here](https://f1000research.com/articles/6-596/v1).

<a id="getting-started">
## How do I get started?

- [Ideogram.js Documentation](https://eweitz.github.io/ideogram/) served via GitHub pages on the site.
- [Ideogram.js Slides](https://speakerdeck.com/eweitz/designing-genome-visualizations-with-ideogramjs) "Visualizations with Ideogram.js"
- [Ideogram.js on GitHub](https://github.com/eweitz/ideogram/)
- [Ideogram.js: Chromosome visualization with JavaScript](https://speakerdeck.com/eweitz/ideogramjs-chromosome-visualization-with-javascript) October 2018
- [Designing genome visualizations with Ideogram.js](https://speakerdeck.com/eweitz/designing-genome-visualizations-with-ideogramjs), April 2020


<a id="contribute">
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