varri-js 1.0.1 → 1.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CITATION.bib +3 -3
- package/CITATION.cff +4 -4
- package/README.html +4 -4
- package/README.md +55 -37
- package/citation.html +5 -5
- package/doc/vaRRI-UI-example.png +0 -0
- package/docu.free-trailing-ends.md +3 -3
- package/example-data.js +1 -1
- package/index.html +7 -7
- package/logo/vaRRI.logo.svg +21 -13
- package/logo/vaRRI.media.png +0 -0
- package/package.json +4 -4
- package/src/README.md +1 -1
- package/doc/example-page-screenshot.png +0 -0
- package/doc/vaRRI_example_output.png +0 -0
- package/doc/vaRRI_example_output.svg +0 -8
package/CITATION.bib
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@misc{raden_varrii_js_2026,
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title = {vaRRI
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title = {vaRRI - Visual annotation of RNA-RNA interactions},
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author = {Raden, Martin and Ganter, Fabian},
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year = {2026},
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url = {https://backofenlab.github.io/vaRRI
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url = {https://backofenlab.github.io/vaRRI/},
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note = {Web application and JavaScript library},
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abstract = {vaRRI
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abstract = {vaRRI is a browser-based JavaScript library for visualizing RNA-RNA interactions (RRIs) as 2D diagrams with annotations such as base-pair highlights, probability profiles, subsequence highlights, and point mutation annotations.},
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keywords = {RNA, RNA-RNA interaction, visualization, JavaScript, bioinformatics},
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version = {1.0.0},
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license = {MIT},
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package/CITATION.cff
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cff-version: 1.2.0
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title: vaRRI
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title: vaRRI - Visual annotation of RNA-RNA interactions
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message: >-
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If you use this software in a publication, please cite it using the metadata
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in this file.
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website: 'https://www.bioinformatics.uni-freiburg.de/'
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version: 1.0.0
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date-released: '2026-07-31'
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repository-code: 'https://github.com/BackofenLab/vaRRI
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url: 'https://backofenlab.github.io/vaRRI
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repository-code: 'https://github.com/BackofenLab/vaRRI'
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url: 'https://backofenlab.github.io/vaRRI/'
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abstract: >-
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vaRRI
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vaRRI is a browser-based JavaScript library for visualizing RNA-RNA
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interactions (RRIs) as 2D diagrams with annotations such as base-pair
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highlights, probability profiles, subsequence highlights, and point mutation
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annotations.
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package/README.html
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>vaRRI
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<title>vaRRI README</title>
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<link rel="icon" type="image/png" href="logo/vaRRI.logo.40x40.png">
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/github-markdown-css/5.5.1/github-markdown.min.css">
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if (isLocalFile && token.type === 'html' && typeof token.text === 'string' && token.text.includes('<iframe')) {
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// Optionally extract the URL from the iframe if present
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const srcMatch = token.text.match(/src=["']([^"']+)["']/);
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const iframeUrl = srcMatch ? srcMatch[1] : 'https://backofenlab.github.io/vaRRI
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const iframeUrl = srcMatch ? srcMatch[1] : 'https://backofenlab.github.io/vaRRI/index.html';
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token.text = `
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<div class="status-banner" style="margin: 16px 0;">
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// 3. Define URLs
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const localUrl = './README.md';
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const remoteUrl = 'https://raw.githubusercontent.com/BackofenLab/vaRRI
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const remoteUrl = 'https://raw.githubusercontent.com/BackofenLab/vaRRI/main/README.md';
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// 4. Choose target URL
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const targetUrl = isLocalFile ? remoteUrl : localUrl;
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⚠️ <strong>Note:</strong>
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<blockquote style="margin: 8px;">
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README.html was opened locally and cannot access the local README.md.<br>
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Therefore, the README was loaded from the <a href="${remoteUrl}">vaRRI
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Therefore, the README was loaded from the <a href="${remoteUrl}">vaRRI online repository</a>.
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</blockquote>
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</div>
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`;
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package/README.md
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#
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# vaRRI - Visual Annotation of RNA–RNA Interactions
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Visualise and annotate RNA–RNA interactions directly in the browser — no server or no command-line tools required.
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 Visualise and annotate RNA–RNA interactions directly in the browser — no server or no command-line tools required.
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---
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## Table of Contents
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1. [Overview](#overview-and-objective)
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2. [Examples from Literature](#examples-from-literature-reproduced-with-varri
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2. [Examples from Literature](#examples-from-literature-reproduced-with-varri)
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3. [Project Structure](#project-structure)
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4. [Quick Start](#quick-start)
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5. [npm Package](#npm-package)
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## Overview and Objective
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vaRRI
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vaRRI is a pure JavaScript library to visualize the base pairing of
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RNA-RNA interactions (RRIs) as 2D diagrams with additional annotation like
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- coloring by sequence or loop type,
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> If you like it, [please cite it!](citation.html)
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Given two sequences and the RRI secondary-structure encoding in dot-bracket notation, vaRRI
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Given two sequences and the RRI secondary-structure encoding in dot-bracket notation, vaRRI renders
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them with the [Fornac](https://github.com/ViennaRNA/fornac) library, and then
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applies all of vaRRI's annotations and tweaks.
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[](https://backofenlab.github.io/vaRRI/)
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---
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## Examples from Literature reproduced with vaRRI
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## Examples from Literature reproduced with vaRRI
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To showcase the capabilities of vaRRI
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To showcase the capabilities of vaRRI, we provide a collection of examples from the literature that have been reproduced using vaRRI.
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The examples can be loaded directly in the input website via the **Example** dropdown.
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## Project Structure
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```
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vaRRI
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vaRRI/
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│
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├── fornac/
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│ ├── fornac.js # Fornac library (vaRRI dependency)
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> before using it in a production environment.
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The easiest way to [**use vaRRI
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The easiest way to [**use vaRRI is via the GitHub pages website**](https://BackofenLab.github.io/vaRRI):
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- [https://BackofenLab.github.io/vaRRI
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- [https://BackofenLab.github.io/vaRRI](https://BackofenLab.github.io/vaRRI)
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If you want to run the website locally or use the library in your own HTML page, clone the repository or download a ZIP of the project via the [Releases](https://github.com/BackofenLab/vaRRI
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If you want to run the website locally or use the library in your own HTML page, clone the repository or download a ZIP of the project via the [Releases](https://github.com/BackofenLab/vaRRI/releases) section.
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Afterwards, open `index.html` directly in a browser — no build step or server needed:
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```bash
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git clone https://github.com/BackofenLab/vaRRI
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cd vaRRI
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git clone https://github.com/BackofenLab/vaRRI.git
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cd vaRRI
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# simply open index.html in your browser, e.g.:
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open index.html # macOS
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xdg-open index.html # Linux
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## npm Package
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Install vaRRI
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Install vaRRI in an application with:
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```bash
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npm install varri-js
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```
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The npm package remains `varri-js`; the GitHub repository and project branding are `vaRRI`.
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Version 1.0.2 includes the updated complete viewer as well as the library.
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### Open `index.html` in Browser
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After installation via npm, you find the vaRRI
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After installation via npm, you find the vaRRI user interface `index.html` in the following subfolder
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```bash
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node_modules/varri-js/index.html
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Behaviour of generated list entries:
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- When **RRI Background** is set to `nothing`, no generated region entry is shown.
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- When set to `region`, vaRRI
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- When set to `basepairs`, vaRRI
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- When set to `region`, vaRRI computes the overall intermolecular interaction region and displays it as a generated, non-removable region entry.
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- When set to `basepairs`, vaRRI computes one or more generated region entries that correspond to intermolecular basepair stacks and displays them as non-removable entries.
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- Generated entries are refreshed automatically from the current structure and settings; they are not exported as user-defined region highlights in share links.
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> [!TIP]
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> - For convenience, respective text *files can be dragged and dropped* into the input fields to load the probability profiles.
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> - vaRRI
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> - vaRRI also supports CSV files with a header line, where the first column contains the nucleotide indices and the second column contains the probability values. Such data is automatically converted to the space-separated format above, and the header line is ignored.
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Finally, the following fields are available to define the visualization of the probability profiles:
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### Point Mutations
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RNA-RNA interaction visualizations are often used to discuss the effect of point mutations on the interaction.
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To support this, vaRRI
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To support this, vaRRI allows to define point mutations in the input sequences and visualizes them in the rendered structure.
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A point mutation is defined by the sequence (1 or 2), the index of the nucleotide to mutate, and the new nucleotide (or letter) to use for the mutation.
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This information is provided in the following fields, and the "Add" button registers the mutation.
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| **Color** | The color to use for highlighting the mutated nucleotide. |
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> [!TIP]
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> vaRRI
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> vaRRI allows to define arbitrary letters as mutations, i.e. the mutated nucleotide does not need to be a valid IUPAC character.
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> That way, any kind of annotation can be added to the sequence, e.g. a letter representing a chemical modification, symbols for a certain type of mutation, or even a short word.
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All registered mutations are shown in a list above the input fields, and can be removed by clicking the "🗑️" icon.
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## URL Parameters & Sharing
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**vaRRI
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**vaRRI** supports state persistence directly via URL parameters, allowing you to pre-fill inputs or share specific visualization configurations using the **🔗 Share Link** button in the export panel. Most parameter names map directly to their corresponding HTML element IDs.
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### Key Parameters
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You can embed the visualization directly into external web pages (e.g., in documentation, blogs, or web tools) using an `<iframe>`.
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### Embeddings in Existing Web Applications
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Currently, vaRRI is already available as an RRI visualizer in the the following web applications:
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- Freiburg RNA Tools: [https://rna.informatik.uni-freiburg.de/](https://rna.informatik.uni-freiburg.de/)
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- IntaRNA - RNA-RNA interaction prediction server
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- [Example visualization](https://rna.informatik.uni-freiburg.de/IntaRNA/Result.jsp?toolName=IntaRNA&jobID=4267751)
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- CopomuS - Compensatory Mutation Designer for RNA-RNA interactions
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- [Example visualization](https://rna.informatik.uni-freiburg.de/CopomuS/Result.jsp?toolName=CopomuS&jobID=1595284)
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- Galaxy Visualizer: [https://usegalaxy.eu/](https://usegalaxy.eu/)
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- vaRRI is available as a visualization tool for RNA-RNA interactions in the Galaxy workflow system
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### Query Parameter
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Use the `showRenderingOnly=true` URL parameter to hide all surrounding UI elements (header, controls panel, footer) and display only the visualization result panel.
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```text
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https://backofenlab.github.io/vaRRI
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https://backofenlab.github.io/vaRRI/index.html?showRenderingOnly=true&<remaining_parameters...>
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```
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For embedding without header and footer, you can also use the `hideFooterAndHeader=true` parameter, which will hide the header and footer but keep the controls panel visible, i.e. this checks the "Full screen UI" checkbox in the controls panel.
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```html
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<iframe
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src="https://backofenlab.github.io/vaRRI/?sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29&showRenderingOnly=true"
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style="border: none;"
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title="vaRRI
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title="vaRRI Visualization">
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</iframe>
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```
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> [!IMPORTANT]
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> Ensure special characters in URL parameters (such as `&` separating two RNA strands) are properly URL-encoded as `%26` when constructing embedding links manually. Also `()` have to be encoded using `%28` and `%29` respectively, as they are not encoded by default by URL encoders following RFC 3986.
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Valid embedding links can be generated using the "🔗 Share Link" button in the vaRRI
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Valid embedding links can be generated using the "🔗 Share Link" button in the vaRRI interface but have to extended with `&showRenderingOnly=true`.
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----
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<iframe
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src="https://backofenlab.github.io/vaRRI
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src="https://backofenlab.github.io/vaRRI/?showRenderingOnly=true&sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29"
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style="border: 2px solid #333333; border-radius: 6px;"
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title="vaRRI
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title="vaRRI Visualization">
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----
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> * If you are viewing [this page on **GitHub Pages**](https://backofenlab.github.io/vaRRI/README.html), the live widget will render directly below.
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## Input Format Reference
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### Dot-Bracket Notation
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vaRRI
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vaRRI accepts standard dot-bracket secondary structure notation with the following characters:
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| Character | Meaning |
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The only restriction is that the brackets must be balanced, i.e. every opening bracket must have a corresponding closing bracket of the same type.
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> [!IMPORTANT]
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> In that case, the primary layout will be based on a reduced set of basepairs that do not cross each other, and the remaining basepairs are added subsequently.
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> Therefore, the layout of pseudoknotted structures may not be optimal, and the visualisation may be less clear than for non-pseudoknotted structures.
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Include `src/vaRRI.js` after the Fornac dependencies.
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The library exposes a single global object `vaRRI` with the a set of respective functions.
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The `src` directory provides a [detailed vaRRI
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The `src` directory provides a [detailed vaRRI Library API documentation](src/README.md)
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---
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## Release Process
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Publishing is automated by [`.github/workflows/publish-npm.yml`](https://github.com/BackofenLab/vaRRI
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Publishing is automated by [`.github/workflows/publish-npm.yml`](https://github.com/BackofenLab/vaRRI/blob/main/.github/workflows/publish-npm.yml).
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Releases continue to update the existing `varri-js` npm package. The npm package name is
|
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independent of the GitHub repository name; no source files need to be renamed.
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An owner must configure a **GitHub Actions trusted publisher** in the `varri-js` package's npm settings:
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organization `BackofenLab`, repository `vaRRI`, workflow filename `publish-npm.yml`, no
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environment name, with direct `npm publish` allowed. This one-time account action may request
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2FA. The workflow uses OIDC and does not require an `NPM_TOKEN` secret or interactive 2FA for
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each release. See [npm trusted publishing](https://docs.npmjs.com/trusted-publishers/).
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After the GitHub repository rename, update any existing trusted publisher that still names
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the old repository to `vaRRI`. The repository name is case-sensitive.
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Merge the workflow changes before creating a release tag on a commit containing them.
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Every published GitHub release runs the tests, derives the npm version from the release tag,
|
package/citation.html
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<title>Citation — vaRRI</title>
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<!-- External Stylesheets (matching index.html) -->
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<a class="group-logo-link" href="https://www.bioinf.uni-freiburg.de" target="_blank" rel="noopener noreferrer" aria-label="Visit the Bioinformatics Group Freiburg website">
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<img class="group-logo" src="https://www.bioinf.uni-freiburg.de/assets/images/bioinf-fr-logo-blau.png" alt="Bioinformatics Group Freiburg logo" />
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</a>
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<img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI
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<img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI logo">
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<div class="header-title">
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<h1>vaRRI
|
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<h1>vaRRI</h1>
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<p>Visual Annotation of RNA–RNA Interactions</p>
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</div>
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<div class="uni-logo-wrap">
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</p>
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<p>
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The source code for this service is freely available on
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<a href="https://github.com/BackofenLab/vaRRI
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<a href="https://github.com/BackofenLab/vaRRI" target="_blank" rel="noopener noreferrer">GitHub</a>.
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<script>
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const TABS_CONFIG = {
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bibtex: { label: 'BibTeX', filename: 'CITATION.bib', mime: 'text/plain', source: 'CITATION.bib', type: 'raw' },
|
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|
Binary file
|
|
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|
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# "Free trailing ends" feature — documentation
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This document describes the "Free trailing ends" feature of vaRRI
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This document describes the "Free trailing ends" feature of vaRRI: what it
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does, the relevant parts of Fornac's internal force-layout architecture it
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depends on, and the exact steps taken to implement it.
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## 1. What the feature does
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vaRRI
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vaRRI renders RNA/RNA-RNA-interaction structures using
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[Fornac](https://github.com/ViennaRNA/fornac)'s force-directed layout
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(`options.forceLayout = true`, i.e. the "Enable Fornac force-layout animation"
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checkbox). Fornac's layout algorithm pulls every *loop* of the structure
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"Enable Fornac force-layout animation" is also enabled), vaRRI
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"Enable Fornac force-layout animation" is also enabled), vaRRI removes this
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artificial circularisation from the force simulation:
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name: 'RNA–RNA interaction feature overview',
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nameShort: 'All feature showcase',
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description: 'Demonstrates cropping, probability profiles, region and subsequence highlights, and point mutations in one interaction.',
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descriptionShort: 'Showcases all features of vaRRI
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descriptionShort: 'Showcases all features of vaRRI.',
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vaRRIParams: {
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sequence: 'ACGAUCAUGUGGUUUAGAGCAUUUUCGACAGCAG&ACGAAAAAAAGAGCAGACAGUAG',
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|
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<title>vaRRI — Visual Annotation of RNA-RNA Interactions</title>
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<!-- vaRRI
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<!-- vaRRI UI -->
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<a class="group-logo-link" href="https://www.bioinf.uni-freiburg.de" target="_blank" rel="noopener noreferrer" aria-label="Visit the Bioinformatics Group Freiburg website">
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<img class="group-logo" src="https://www.bioinf.uni-freiburg.de/assets/images/bioinf-fr-logo-blau.png" alt="Bioinformatics Group Freiburg logo">
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<img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI
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<img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI logo">
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<h1>vaRRI
|
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<h1>vaRRI</h1>
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|
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<button id="exportSvgBtn" class="btn btn-success btn-sm" type="button" title="Download rendering in SVG format.">⬇ SVG</button>
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<button id="openVarriBtn" class="btn btn-openVarri btn-sm" type="button" title="Show this in a new vaRRI
|
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<button id="openVarriBtn" class="btn btn-openVarri btn-sm" type="button" title="Show this in a new vaRRI browser window">Full Page</button>
|
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<!-- right-aligned note to cite varri-->
|
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<span class="cite-note">Please
|
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|
-
<a href="citation.html" class="btn btn-cite btn-sm">🔖 cite vaRRI
|
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|
+
<a href="citation.html" class="btn btn-cite btn-sm">🔖 cite vaRRI</a></span>
|
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</section>
|
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|
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The source code for this service is freely available on
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<a href="https://github.com/BackofenLab/vaRRI
|
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+
<a href="https://github.com/BackofenLab/vaRRI" target="_blank" rel="noopener noreferrer">GitHub</a>.
|
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|
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+
style="font-weight:800;font-size:80px;font-family:'-apple-system', BlinkMacSystemFont, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif;dominant-baseline:central;text-anchor:middle;fill:#4d4d4d;stroke-width:0.868952"
|
|
149
|
+
id="path840" />
|
|
150
|
+
</g>
|
|
143
151
|
</g>
|
|
144
152
|
</svg>
|
package/logo/vaRRI.media.png
CHANGED
|
Binary file
|
package/package.json
CHANGED
|
@@ -1,16 +1,16 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "varri-js",
|
|
3
|
-
"version": "1.0.
|
|
3
|
+
"version": "1.0.2",
|
|
4
4
|
"description": "Browser viewer and JavaScript library for visualising and annotating RNA-RNA interactions",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"author": "Bioinformatics Group, University of Freiburg",
|
|
7
|
-
"homepage": "https://backofenlab.github.io/vaRRI
|
|
7
|
+
"homepage": "https://backofenlab.github.io/vaRRI/",
|
|
8
8
|
"repository": {
|
|
9
9
|
"type": "git",
|
|
10
|
-
"url": "git+https://github.com/BackofenLab/vaRRI
|
|
10
|
+
"url": "git+https://github.com/BackofenLab/vaRRI.git"
|
|
11
11
|
},
|
|
12
12
|
"bugs": {
|
|
13
|
-
"url": "https://github.com/BackofenLab/vaRRI
|
|
13
|
+
"url": "https://github.com/BackofenLab/vaRRI/issues"
|
|
14
14
|
},
|
|
15
15
|
"keywords": [
|
|
16
16
|
"bioinformatics",
|
package/src/README.md
CHANGED
|
Binary file
|
|
Binary file
|