dms-view
dms-view: Interactive visualization tool for deep mutational scanning data - Published in JOSS (2020)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: biorxiv.org, joss.theoj.org, zenodo.org -
✓Committers with academic emails
7 of 17 committers (41.2%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords from Contributors
Repository
Interactive visualization of mutational antigenic profiling data
Basic Info
- Host: GitHub
- Owner: dms-view
- License: mit
- Language: JavaScript
- Default Branch: master
- Homepage: http://dms-view.github.io/
- Size: 43.5 MB
Statistics
- Stars: 10
- Watchers: 4
- Forks: 6
- Open Issues: 25
- Releases: 2
Metadata Files
README.md
dms-view
Sarah Hilton*, John Huddleston*, Allison Black, Khrystyna North, Adam Dingens, Trevor Bedford, and Jesse Bloom. (* equal contribution)
dms-view is an interactive visualization tool for deep mutational scanning experiments.
You can find the tool at dms-view.github.io.
This repo contains the JavaScript and D3 code to run the tool itself. For information on how to use the tool, please see the documentation.
Please raise issues with the tool at github.com/dms-view/dms-view.github.io/issues.
Organization
The code and data for the docs, the tool, and the paper are found in the following directories:
./assets/
This directory contains the code for the dms-view.github.io tool.
- ./assets/css/ contains the CSS stylesheet.
- ./assets/fonts/ contains the font file for the logoplots
- ./assets/images/ contains static images used in the docs and the tool.
- ./assets/js/ contains the JavaScript code to run the tool.
./data/
This directory contains the default data for the tool from Lee et al., 2019.
./docs/
This directory contains the code for the dms-view docs.
./_layouts/
This directory contains the templates for the docs.
./paper/
This directory contains the code for the dms-view paper.
Testing
As described above, dms-view uses a default dataset from Lee et al., 2019.
Below are two descriptions of different combinations of dropdown menus and selected sites, as well as pictures of what the tool should look like.
View 1 (default view)
When dms-view.github.io is loaded, the default view of the data section should look as follows:
Load view 1 to explore this example.
View 2
The data section should look as follows when you change - condition to "2009-age-65" - mutation metric to "Natural Frequencies" - selected sites 144, 159, 192, 193, 222, 224
Load view 2 to explore this example.
Other views
In the documentation, we use dms-view to recreate paper figures for two different studies.
Please see dms-view.github.io/docs/casestudies to see these examples
Contribute to dms-view
We welcome contributions to the dms-view code and documentation.
Consult our contributing guide for more details.
Have you used dms-view for your own analyses and think these would make a great case study for our documentation?
Open a new issue on GitHub to let us know more.
Building the complete website locally
Build the complete dms-view website locally with Jekyll and Bundler.
```bash
Install dependencies for Jekyll.
bundle install
Build the site.
bundle exec jekyll serve ```
View the local website in your browser at http://localhost:4000/.
See the documentation for more details on deploying or developing dms-view locally.
Owner
- Name: dms-view
- Login: dms-view
- Kind: organization
- Email: skhilton@uw.edu
- Website: dms-view.github.io
- Repositories: 3
- Profile: https://github.com/dms-view
Interactive visualization tool for deep mutational scanning.
JOSS Publication
dms-view: Interactive visualization tool for deep mutational scanning data
Authors
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Molecular and Cell Biology, University of Washington, Seattle, WA, USA
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, University of Washington, Seattle, WA, USA
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA, Howard Hughes Medical Institute, Seattle, WA, USA
Editor
Charlotte Soneson
Tags
Javascript D3 molecular biology protein evolution data visualizationGitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| skhilton | s****n@u****u | 321 |
| John Huddleston | h****j@g****m | 170 |
| kdilai | k****i@g****m | 24 |
| Khrystyna Dilai | k****i@k****n | 11 |
| Alli Black | b****i@g****m | 6 |
| jbloom | j****m@f****g | 5 |
| Khrystyna Dilai | k****i@k****g | 4 |
| Sarah | s****n@M****l | 3 |
| Khrystyna Dilai | k****i@D****u | 2 |
| Khrystyna Dilai | k****i@D****u | 2 |
| Khrystyna Dilai | k****i@D****u | 1 |
| Khrystyna Dilai | k****i@D****u | 1 |
| Khrystyna Dilai | k****i@D****u | 1 |
| Sarah Hilton | s****n@S****l | 1 |
| Yang Liu | y****0@c****u | 1 |
| Thomas Sibley | t****y@f****g | 1 |
| Charlotte Soneson | c****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 63
- Total pull requests: 44
- Average time to close issues: about 1 month
- Average time to close pull requests: 3 days
- Total issue authors: 7
- Total pull request authors: 5
- Average comments per issue: 0.98
- Average comments per pull request: 0.61
- Merged pull requests: 41
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- huddlej (22)
- skhilton (17)
- jbloom (9)
- thorvere (5)
- afrubin (5)
- andrefaure (4)
- adingens (1)
Pull Request Authors
- skhilton (25)
- huddlej (16)
- tsibley (1)
- dependabot[bot] (1)
- csoneson (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- github-pages ~> 206 development
- minima ~> 2.5
- tzinfo ~> 1.2
- tzinfo-data >= 0
- wdm ~> 0.1.1