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https://github.com/cnpem/ddx3x-stress-granules-analyses

https://github.com/cnpem/ddx3x-stress-granules-analyses

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

DDX3X Stress Granules Analysis

This repository contains the analysis pipeline for investigating stress granules in DDX3X variants using microscopy data. The analysis includes cell segmentation, stress granule detection, and statistical analysis of granule properties.

Prerequisites

  1. Install uv for Python package management
  2. Install Quarto for report generation

Setup

  1. Clone this repository: bash git clone https://github.com/username/ddx3x-stress-granules-analyses.git cd ddx3x-stress-granules-analyses

  2. Use uv sync to create a virtual environment and install depedencies: bash uv sync

  3. Activate the virtual environment: bash source .venv/bin/activate

Data

The microscopy data is not included in this repository due to size constraints but is available on Zenodo DOI.

Running the Analysis

Generate the analysis report using Quarto: bash quarto render . --output-dir report

This will create a report directory containing the complete analysis. Open report/index.html in your web browser to view the results.

Directory Structure

  • data/: Raw microscopy images (not included in repository)
  • figures/: Generated images showing three processing stages for each analyzed image:
    1. Maximum intensity projection
    2. Filtered channel
    3. Cell and granule detection results
  • output/: CSV files containing:
    • granule_area.csv: Measurements of individual stress granules
    • granules_per_cell.csv: Cell-level granule counts and metrics
  • plots/: Generated plots and visualizations including:
    • Violin plots comparing granule areas across conditions
    • Violin plots showing granule count distributions
    • Bar plots of cell percentages with different granule counts
  • report/: Generated analysis report (after running Quarto)

Owner

  • Name: Brazilian Center for Research in Energy and Materials (CNPEM)
  • Login: cnpem
  • Kind: organization
  • Location: Brazil

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Public event: 1
  • Push event: 1
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Public event: 1
  • Push event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 13
  • Total Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 13
  • Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jose Geraldo de Carvalho Pereira z****o@o****m 13

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • zgcarvalho (1)
Pull Request Authors
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Dependencies

pyproject.toml pypi
  • cellpose ==3.1.0
  • imageio >=2.36.0
  • jupyter >=1.1.1
  • llvmlite ==0.43
  • matplotlib >=3.9.2
  • microfilm >=0.2.1
  • pandas >=2.2.3
  • pingouin >=0.5.5
  • scikit-image >=0.24.0
  • seaborn >=0.13.2
  • torch >=2.5.1