Data

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Open Source Science

https://github.com/broadinstitute/jump_hub

The one-stop-shop for Morphological Profiling and JUMP Cell-Painting

https://github.com/broadinstitute/jump_hub

Science Score: 26.0%

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.3%) to scientific vocabulary

Keywords

compbio profiling
Last synced: 5 months ago · JSON representation

Repository

The one-stop-shop for Morphological Profiling and JUMP Cell-Painting

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: cc0-1.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 446 MB
Statistics
  • Stars: 7
  • Watchers: 11
  • Forks: 2
  • Open Issues: 8
  • Releases: 0
Topics
compbio profiling
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License

readme.md

JUMP hub

Repository to generate the one-in-all resource for morphological profiling, specialized in data from JUMP Cell Painting. Here is the main website.

This repository generates the website and also contains the dependencies to run the notebooks and ensure their correctness.

Notes

Additionally, this repository can be used as a way to install essential dependencies for an exploratory analysis of JUMP morphological data.

Python notebooks are in the colab branch. Notebooks are autogenerated using these scripts.

Contributing

See CONTRIBUTING.md for development setup and testing.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 42
  • Watch event: 4
  • Delete event: 25
  • Issue comment event: 99
  • Push event: 239
  • Pull request review comment event: 20
  • Pull request review event: 40
  • Pull request event: 47
  • Fork event: 1
  • Create event: 15
Last Year
  • Issues event: 42
  • Watch event: 4
  • Delete event: 25
  • Issue comment event: 99
  • Push event: 239
  • Pull request review comment event: 20
  • Pull request review event: 40
  • Pull request event: 47
  • Fork event: 1
  • Create event: 15

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 46
  • Total pull requests: 61
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 8
  • Total pull request authors: 8
  • Average comments per issue: 7.63
  • Average comments per pull request: 1.0
  • Merged pull requests: 31
  • Bot issues: 0
  • Bot pull requests: 21
Past Year
  • Issues: 30
  • Pull requests: 38
  • Average time to close issues: 18 days
  • Average time to close pull requests: 3 days
  • Issue authors: 5
  • Pull request authors: 6
  • Average comments per issue: 1.43
  • Average comments per pull request: 1.03
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • AnneCarpenter (19)
  • shntnu (5)
  • afermg (5)
  • mtcaton (1)
  • bethac07 (1)
Pull Request Authors
  • dependabot[bot] (21)
  • AnneCarpenter (14)
  • shntnu (10)
  • PaulaLlanos (7)
  • ErinWeisbart (4)
  • afermg (3)
  • jessica-ewald (2)
  • HugoHakem (1)
Top Labels
Issue Labels
orf (3) crispr (2) no-evidence (1) new story we will include (1) internal (1) On hold (1) enhancement (1)
Pull Request Labels
dependencies (21) bug (1)

Dependencies

requirements.txt pypi
  • jump_deps ==0.0.7
.github/workflows/build_website.yml actions
  • DeterminateSystems/magic-nix-cache-action main composite
  • DeterminateSystems/nix-installer-action main composite
  • actions/checkout v3 composite
poetry.lock pypi
  • 156 dependencies
pyproject.toml pypi
  • jupyter ^1.0.0 develop
  • jupytext ^1.15.0 develop
  • pytest ^7.4.1 develop
  • ruff <0.2.0 develop
  • ruff-lsp ^0.0.48 develop
  • biopython ^1.84
  • boto3 >=1.33.1
  • broad-babel ^0.1.24
  • ipdb ^0.13.13
  • matplotlib ^3.8.2
  • polars >=0.19.19
  • pyarrow >=15.0.0
  • python >=3.10,<3.12
  • s3fs >=2023.12.1
  • seaborn ^0.13.2