igv-jupyter
dash-bio
| igv-jupyter | dash-bio | |
|---|---|---|
| 1 | 2 | |
| 154 | 513 | |
| 0.0% | 1.6% | |
| 1.8 | 3.7 | |
| over 1 year ago | 3 months ago | |
| JavaScript | Python | |
| MIT License | MIT License |
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igv-jupyter
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Bam viewer with custom fasta reference that's embeddable in Streamlit app?
igv-notebook and igv-jupyter seem amazing but (unsurprisingly) I could not get them to run anywhere that wasn't a jupyter notebook. I get a kernel error as it tries to initialize itself within streamlit, and I'm not sure how to embed it anywhere else.
dash-bio
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Bam viewer with custom fasta reference that's embeddable in Streamlit app?
dash-bio This is another great choice, but unlike standard plotly figures, I need to find how to embedd dash widgets into streamlit. It seems possible, but it's not clear how to do it.
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New CRISPR-based map ties every human gene to its function
> Where are the polished, powerful design tools for biology
User interfaces for biology have drastically improved over the last 10 years.
Domain-specific tools like genome browsers, protein viewers, or phylogenetic explorers [1-3] almost all look and feel a lot better than they did in 2012.
The biggest exception here is UCSC Genome Browser, which has an old-school design and web technology stack. That said, it's steadily added features over the years, has substantially sleekened UX in its periphery, and remains widely used.
There are also bespoke visual design resources for biology applications that are good and getting better, like BioRender and PhyloPic [4-5]. There are multi-tiered packages like Dash Bio that wrap biology components together. There's Blender biology community, too!
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1. Genome browsers and components: https://jbrowse.org/jb2/, https://www.ncbi.nlm.nih.gov/genome/gdv, https://igv.org/app, https://eweitz.github.io/ideogram
2. Protein viewers: https://pymol.org/, https://nglviewer.org/ngl/
3. Phylogenetic explorers: https://clades.nextstrain.org/
4. https://biorender.com/
5. http://phylopic.org/
6. https://github.com/plotly/dash-bio, https://dash.gallery/Portal/?search=[Pharma]
What are some alternatives?
configurable-http-proxy - node-http-proxy plus a REST API
tinycov - Command line tool to plot genomic coverage from a BAM file
ipyigv - A Jupyter wrapper for the igv.js library (representation of genomic data)
pybamview - Browser based application for viewing bam alignments
igv-notebook - Module for embedding igv.js in an IPython notebook
kuwala - Kuwala is the no-code data platform for BI analysts and engineers enabling you to build powerful analytics workflows. We are set out to bring state-of-the-art data engineering tools you love, such as Airbyte, dbt, or Great Expectations together in one intuitive interface built with React Flow. In addition we provide third-party data into data science models and products with a focus on geospatial data. Currently, the following data connectors are available worldwide: a) High-resolution demographics data b) Point of Interests from Open Street Map c) Google Popular Times
ipyleaflet - A Jupyter - Leaflet.js bridge