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tsspredator-web

TSSpredator-Web allows a web-based TSS predicition for prokaryotic data.

https://github.com/integrative-transcriptomics/tsspredator-web

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

TSSpredator-Web allows a web-based TSS predicition for prokaryotic data.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

TSSpredator-Web

DOI

Short overview

A web-application for the predication of Transcription Starting Sites (TSS) using Wiggle files and TSSpredator.

Besides facilitating the overall prediction of the TSS by providing a web-application, the interface facilitates the file allocation by allowing a drag-and-drop distribution of the files. Moreover, all config files can be saved and easily uploaded for any re-anaysis of the data.

While predicting the TSSs, a status website is provided. This allows users to close the browser without interrupting the prediction of the TSSs.

The application also allows the exploration of the results by providing overview and detail visualizations.

All results and figures can be also exported from the web-app.

TSSpredator-Web is available at: https://tsspredator-tuevis.cs.uni-tuebingen.de/

Local usage

You can also use TSSpredator in your own computer

Requirements

  • Yarn (v4.1.1)
  • mamba/conda
  • java (v20.0.1)

Running locally

bash bash setup.sh yarn run tsspredator

We also provide Docker images for faster usage.

  • Make sure your Docker engine is running.
  • Download the latest releases.

  • Set up the variables_tsspredator.env to indicate:

    1) The path of the example files (This is only required if you want to use the example files) 2) The path for your redis database (this can be anywhere)

  • Run:

```bash

load the images from the tar file

docker load --input TSSpredatorCelery docker load --input TSSpredatorWeb

run the container

docker compose --env-file variables_tsspredator.env up -d ```

Owner

  • Name: Integrative-Transcriptomics
  • Login: Integrative-Transcriptomics
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Joe
  given-names: Johnson
orcid: https://orcid.org/0000-0000-0000-0000
title:Integrative-Transcriptomics/TSSpredator-Web: Publishing version of TSSpredator-Web
version: v1.0.0
date-released: 2025-05-27

GitHub Events

Total
  • Release event: 2
  • Watch event: 1
  • Delete event: 10
  • Issue comment event: 2
  • Push event: 45
  • Pull request review comment event: 2
  • Pull request review event: 3
  • Pull request event: 48
  • Create event: 16
Last Year
  • Release event: 2
  • Watch event: 1
  • Delete event: 10
  • Issue comment event: 2
  • Push event: 45
  • Pull request review comment event: 2
  • Pull request review event: 3
  • Pull request event: 48
  • Create event: 16

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 0
  • Total pull requests: 22
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 22
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 1
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Top Authors
Issue Authors
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  • mwittep (21)
  • dependabot[bot] (1)
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dependencies (1)

Dependencies

.github/workflows/docker.yml actions
  • actions/checkout v4 composite
.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
  • shimataro/ssh-key-action v2.3.1 composite
docker-compose.yml docker
  • redis alpine
  • tsspredator_celery_app latest
  • tsspredator_web latest
package-lock.json npm
  • 1694 dependencies
package.json npm
  • @babel/plugin-proposal-private-property-in-object ^7.16.7 development
  • @testing-library/jest-dom ^5.16.4
  • @testing-library/react ^13.1.1
  • @testing-library/user-event ^13.5.0
  • @upsetjs/react ^1.11.0
  • gosling.js ^0.13.2
  • higlass ^1.13.3
  • http-proxy-middleware ^2.0.6
  • install ^0.13.0
  • jszip ^3.10.0
  • npm-run-all ^4.1.5
  • pixi.js ^6.5.10
  • plotly.js-cartesian-dist-min ^2.12.1
  • react ^18.0.0
  • react-dom ^18.0.0
  • react-plotly.js ^2.5.1
  • react-router-dom ^6.3.0
  • react-scripts 5.0.1
  • react-spinners ^0.12.0
  • react-table ^7.8.0
  • web-vitals ^2.1.4
requirements.txt pypi
  • Flask ==2.3.3
  • celery ==5.3.4
  • gunicorn ==20.1.0
  • python-dotenv ==0.20.0
  • redis ==3.5.3
  • werkzeug ==2.3.8
setup.py pypi
  • flask *