igv-notebook
dash-bio
| igv-notebook | dash-bio | |
|---|---|---|
| 1 | 2 | |
| 56 | 517 | |
| - | 1.0% | |
| 5.0 | 3.7 | |
| 8 months ago | 4 months ago | |
| JavaScript | Python | |
| MIT License | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
igv-notebook
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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?
igv-jupyter - Extension for Jupyter which integrates igv.js
ipyigv - A Jupyter wrapper for the igv.js library (representation of genomic data)
tinycov - Command line tool to plot genomic coverage from a BAM file
pybamview - Browser based application for viewing bam alignments