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https://github.com/slowkow/cellguide
🧠Navigate single-cell RNA-seq datasets in your web browser.
https://github.com/slowkow/cellguide
bioinformatics cellbrowser data-visualization javascript scrna-seq
Last synced: 2 months ago
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🧠Navigate single-cell RNA-seq datasets in your web browser.
- Host: GitHub
- URL: https://github.com/slowkow/cellguide
- Owner: slowkow
- License: gpl-3.0
- Created: 2020-06-02T17:34:13.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-07-13T15:02:29.000Z (over 1 year ago)
- Last Synced: 2024-05-09T10:27:08.139Z (8 months ago)
- Topics: bioinformatics, cellbrowser, data-visualization, javascript, scrna-seq
- Language: JavaScript
- Homepage: https://cell.guide
- Size: 4.01 MB
- Stars: 25
- Watchers: 4
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Cell Guide ðŸ§
[](https://zenodo.org/badge/latestdoi/268866845)
Navigate single-cell RNA-seq datasets in your web browser.
Try it at https://cell.guide
### Features
- Display metadata on the UMAP figure
- Display gene expression on the UMAP figure
- Aggregate statistics for cell clusters and metadata categories
- Find any gene, instantly
- Browse statistics for every gene
Flip through metadata variables and see them in low-dimensional space.
See which donors have similar proportions of different cell clusters.
Find any gene and see expression across clusters, faceted by metadata variables.
Demo scRNA-seq data from the research article by [Smillie et al. 2019][3].
[3]: https://doi.org/10.1016/j.cell.2019.06.029
## Quick Start
### Step 1. Install Cell Browser
We can install the Cell Browser Python package with pip (we need a specific version):
```
pip install cellbrowser==0.7.15
```
Or see the [Cell Browser installation instructions](https://cellbrowser.readthedocs.io/installation.html).
### Step 2. Create a browser for your data
See the [documentation][1] for how to create a Cell Browser for your data.
When your browser is working, it should look something like this:
### Step 3. Copy Cell Guide files
```bash
# Get the Cell Guide code
curl -s https://codeload.github.com/slowkow/cellguide/tar.gz/master | tar xvz
# Overwrite the Cell Browser files: index.html js/ css/ ext/ img/
command cp -rf cellguide-master/www/* public_html/
```
For a complete example, see the [demo.sh](demo.sh) script.
Make sure to refresh your web browser with ⌘+Shift+R (or Ctrl+Shift+R on Windows).
[1]: https://cellbrowser.readthedocs.io/basic_usage.html
## Dependencies
The current version of Cell Guide depends on [Cell Browser] by [Maximilian
Haeussler].
[Cell Browser]: https://github.com/maximilianh/cellBrowser
[Maximilian Haeussler]: https://github.com/maximilianh
Built with:
- [Bootstrap](https://getbootstrap.com)
- [CSS loaders](https://projects.lukehaas.me/css-loaders/)
- [d3-legend](https://github.com/susielu/d3-legend)
- [D3.js](https://d3js.org)
- [FastBitSet](https://github.com/lemire/FastBitSet.js/)
- [hcluster.js](https://github.com/cmpolis/hcluster.js/)
- [jQuery](https://jquery.com)
- [JSURL2](https://www.npmjs.com/package/@yaska-eu/jsurl2)
- [pako](https://github.com/nodeca/pako)
- [palette.js](https://github.com/google/palette.js/tree/master)
- [papaparse](https://www.papaparse.com/)
- [tablesort](https://github.com/tristen/tablesort)
Let me know what you think! [@slowkow](https://twitter.com/slowkow)