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https://github.com/bhklab/ispy-readii

Running READII on the I-SPY cohort for radiogenomic analysis.

https://github.com/bhklab/ispy-readii

Science Score: 26.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Running READII on the I-SPY cohort for radiogenomic analysis.

Basic Info
  • Host: GitHub
  • Owner: bhklab
  • License: mit
  • Language: HTML
  • Default Branch: main
  • Size: 480 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

ispy-readii

Running READII to perform radiomic feature extraction on the I-SPY cohort for radiogenomic analysis.

Development

Installing Pixi

Pixi is a tool for managing conda environments and managing dependencies.

To install pixi, visit the pixi website and follow the instructions for your operating system.

Cloning the repository

Clone the repository to your local machine using the following command:

bash git clone https://github.com/bhklab/RECIST-play.git

Installing dependencies

To install the dependencies for the handbook, run the following command:

bash pixi install

This will install the dependencies specified in the pixi.toml file.

Adding dependencies

To add a new dependency, run the following command:

bash pixi add <package_name>

This will add the specified package to the pixi.toml file.

Directory Structure

Run the following command in your terminal in the ispy-readii directory to set up the project directory structure: shell mkdir -p procdata rawdata results workflow/{config,envs,logs,notebooks,scripts}

You should now have the following directory structure: bash README.md procdata # output from any processing steps of rawdata rawdata # data as it is downloaded from the source results # final output from the pipeline workflow config envs logs notebooks # Jupyter, R notebooks scripts # Where any code scripts are kept (Python, R, etc.)

Contributing

Please use the following angular commit message format: ``` (optional scope): short summary in present tense

(optional body: explains motivation for the change)

(optional footer: note BREAKING CHANGES here, and issues to be closed)

`` ` refers to the kind of change made and is usually one of:

  • feat: A new feature.
  • fix: A bug fix.
  • docs: Documentation changes.
  • style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc).
  • refactor: A code change that neither fixes a bug nor adds a feature.
  • perf: A code change that improves performance.
  • test: Changes to the test framework.
  • build: Changes to the build process or tools.
  • chore: Other changes that dont modify src or test files (e.g., removing files, updating deps, renaming folders, updating configs)

scope is an optional keyword that provides context for where the change was made. It can be anything relevant to your package or development workflow (e.g., it could be the module or function - name affected by the change).

Owner

  • Name: BHKLAB
  • Login: bhklab
  • Kind: organization
  • Location: Toronto, Ontario, Canada

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total
  • Delete event: 4
  • Push event: 40
  • Pull request event: 8
  • Fork event: 1
  • Create event: 8
Last Year
  • Delete event: 4
  • Push event: 40
  • Pull request event: 8
  • Fork event: 1
  • Create event: 8

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 minutes
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 minutes
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • strixy16 (5)
  • sogolsahebi (1)
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