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https://github.com/amkram/testt

https://github.com/amkram/testt

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Links to: biorxiv.org, pubmed.ncbi, ncbi.nlm.nih.gov
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    Low similarity (11.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: amkram
  • Language: JavaScript
  • Default Branch: master
  • Size: 31.6 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created almost 4 years ago · Last pushed almost 4 years ago
Metadata Files
Readme

README.md

Taxonium

All Contributors

Taxonium is a tool for exploring trees.

➡️ Launch Taxonium

📚 Consult the documentation

📝 Read the preprint

How do I..

visualise my own Newick phylogeny?

Upload a Newick file to Taxonium.org, and optionally a metadata file in CSV or TSV format. If using a metadata file the leftmost column must contain names of the nodes as in the tree.

explore the global SARS-CoV-2 phylogeny?

Visit Cov2Tree.org which uses Taxonium to allow you to explore a tree built by researchers at UCSC using public data contributed by researchers across the world to the INSDC databases.

build my own mutation-annotated tree to explore in Taxonium, or add my own metadata to an existing phylogeny?

Use UShER to build a mutation-annotated tree. Then use taxoniumtools to convert it to a Taxonium format you can upload to the interface at Taxonium.org

You can also use taxoniumtools to add your own metadata to the existing public phylogeny.

Find out more in 📚 the documentation.

See Taxonium in action

Citing Taxonium

Taxonium: a web-based tool for exploring large phylogenetic trees Theo Sanderson bioRxiv 2022.06.03.494608; doi: https://doi.org/10.1101/2022.06.03.494608

N.B. If you are citing the tree displayed at Cov2Tree.org, please cite the UCSC tree (.. and ideally Taxonium too if you relied on it for exploration)

Structure

Taxonium now consists of a number of components:

  • taxoniumtools - a Python package that lets you easily generate Taxonium files from Usher protobuf files
  • taxoniumwebclient - the web client that is available at e.g. taxonium.org and let's you explore Taxonium files in your browser
  • taxonium_backend - a server-based backend that allows Taxonium trees to be explored without the user downloading the full tree (N.B. Taxonium can also be used without this backend, with static files acccessed in taxoniumwebclient)
  • taxoniumdatahandling - this is a node package upon which both the web client and the backend depend (it handles core logic common to both)

Contributors

Taxonium is built and maintained by Theo Sanderson at the Francis Crick Institute.


Theo Sanderson
💻 📖 🎨 🤔 🚇 🚧

We are very grateful to our contributors:


Theo Sanderson
💻 📖 🎨 🤔 🚇 🚧
Angie Hinrichs
🤔 🔣
Richard Goater
🎨 💻
Chaoran Chen
🤔
Cornelius Roemer
🤔
Sung Kwon
🚇

Owner

  • Name: Alex Kramer
  • Login: amkram
  • Kind: user
  • Location: Santa Cruz, CA
  • Company: @corbett-lab

Graduate student at UC Santa Cruz - Biomolecular Engineering and Bioinformatics

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Dependencies

taxonium_backend/package.json npm
  • @jsonlines/core ^1.0.2
  • axios ^0.26.1
  • commander ^9.1.0
  • compression ^1.7.4
  • cors ^2.8.5
  • express ^4.17.3
  • pako ^2.0.4
  • taxonium_data_handling file:../taxonium_data_handling
taxonium_backend/yarn.lock npm
  • @jsonlines/core 1.0.2
  • accepts 1.3.8
  • array-flatten 1.1.1
  • axios 0.26.1
  • body-parser 1.19.2
  • bytes 3.0.0
  • bytes 3.1.2
  • commander 9.1.0
  • compressible 2.0.18
  • compression 1.7.4
  • content-disposition 0.5.4
  • content-type 1.0.4
  • cookie 0.4.2
  • cookie-signature 1.0.6
  • core-js 3.22.2
  • cors 2.8.5
  • debug 2.6.9
  • depd 1.1.2
  • destroy 1.0.4
  • ee-first 1.1.1
  • encodeurl 1.0.2
  • escape-html 1.0.3
  • etag 1.8.1
  • express 4.17.3
  • finalhandler 1.1.2
  • follow-redirects 1.14.9
  • forwarded 0.2.0
  • fresh 0.5.2
  • http-errors 1.8.1
  • iconv-lite 0.4.24
  • inherits 2.0.4
  • ipaddr.js 1.9.1
  • media-typer 0.3.0
  • merge-descriptors 1.0.1
  • methods 1.1.2
  • mime 1.6.0
  • mime-db 1.52.0
  • mime-types 2.1.35
  • ms 2.0.0
  • ms 2.1.3
  • negotiator 0.6.3
  • object-assign 4.1.1
  • on-finished 2.3.0
  • on-headers 1.0.2
  • pako 2.0.4
  • parseurl 1.3.3
  • path-to-regexp 0.1.7
  • proxy-addr 2.0.7
  • qs 6.9.7
  • range-parser 1.2.1
  • raw-body 2.4.3
  • readable-stream 3.6.0
  • readable-web-to-node-stream 3.0.2
  • safe-buffer 5.1.2
  • safe-buffer 5.2.1
  • safer-buffer 2.1.2
  • send 0.17.2
  • serve-static 1.14.2
  • setprototypeof 1.2.0
  • statuses 1.5.0
  • string_decoder 1.3.0
  • taxonium_data_handling 1.0.1
  • toidentifier 1.0.1
  • type-is 1.6.18
  • unpipe 1.0.0
  • util-deprecate 1.0.2
  • utils-merge 1.0.1
  • vary 1.1.2
taxonium_data_handling/package.json npm
  • readable-web-to-node-stream ^3.0.2
taxonium_data_handling/yarn.lock npm
  • inherits 2.0.4
  • readable-stream 3.6.0
  • readable-web-to-node-stream 3.0.2
  • safe-buffer 5.2.1
  • string_decoder 1.3.0
  • util-deprecate 1.0.2
taxonium_web_client/package.json npm
  • eslint-config-standard ^16.0.3 development
  • eslint-plugin-node ^11.1.0 development
  • eslint-plugin-promise ^5.1.0 development
  • postcss 8 development
  • @craco/craco ^6.1.2
  • @tailwindcss/forms ^0.5.2
  • @testing-library/jest-dom ^5.11.4
  • @testing-library/react ^11.1.0
  • @testing-library/user-event ^12.1.10
  • JSONStream ^1.3.5
  • autoprefixer ^9
  • axios ^0.27.2
  • binary-search ^1.3.6
  • classnames ^2.3.1
  • commander ^9.0.0
  • compression ^1.7.4
  • cors ^2.8.5
  • craco ^0.0.3
  • deck.gl ^8.6.6
  • jsonl ^1.1.2
  • lodash ^4.17.21
  • lzma-native ^8.0.6
  • node-polyfill-webpack-plugin ^1.1.4
  • pako ^2.0.4
  • process ^0.11.10
  • react ^17.0.2
  • react-circular-progressbar ^2.0.4
  • react-debounce-input ^3.2.3
  • react-dom ^17.0.2
  • react-hot-toast ^2.2.0
  • react-icons ^4.2.0
  • react-modal ^3.15.1
  • react-router-dom ^5.2.0
  • react-scripts 5.0.0
  • react-spinners ^0.11.0
  • readable-web-to-node-stream ^3.0.2
  • scale-color-perceptual ^1.1.2
  • tailwindcss >=3.1.0
  • taxonium_data_handling file:../taxonium_data_handling
  • web-vitals ^1.0.1
  • webpack ^5.72.0
  • yargs ^17.3.1
taxonium_web_client/yarn.lock npm
  • 1702 dependencies
docs/requirements.txt pypi
  • alive-progress *
  • biopython *
  • furo *
  • google-api-python-client *
  • myst-parser *
  • orjson *
  • pandas *
  • protobuf <4
  • sphinx-argparse *
  • sphinx-book-theme *
  • sphinx-rtd-theme *
  • sphinxcontrib-gtagjs *
  • treeswift *