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Open Source Science

https://github.com/alleninstitute/spatial_compare

package for comparing spatial transcriptomics datasets

https://github.com/alleninstitute/spatial_compare

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary

Keywords from Contributors

interactive projection archival sequences observability autograding hacking shellcodes modular network-simulation
Last synced: 10 months ago · JSON representation

Repository

package for comparing spatial transcriptomics datasets

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 117 MB
Statistics
  • Stars: 6
  • Watchers: 4
  • Forks: 8
  • Open Issues: 15
  • Releases: 0
Created about 2 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

Spatial_Compare

work in progress!

this package is in development and currently unsupported

Comparison of spatial experiments based on matched labels.

image

Not fancy, helpful ™.

to install: To install Spatial_Compare:

  1. Clone the repo and cd into the project directory git clone https://github.com/AllenInstitute/spatial_compare.git cd spatial_compare
  2. Install the required dependencies and install the project: pip install -r requirements.txt pip install .

Alternatively you can install directly from github:

pip install git+https://github.com/AllenInstitute/spatial_compare.git

The example notebook walks through some comparisons across Xenium experiments on marmoset brain.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Create event: 15
  • Issues event: 5
  • Watch event: 4
  • Delete event: 7
  • Member event: 6
  • Issue comment event: 22
  • Push event: 45
  • Public event: 1
  • Pull request review comment event: 3
  • Pull request review event: 11
  • Pull request event: 33
  • Fork event: 5
Last Year
  • Create event: 15
  • Issues event: 5
  • Watch event: 4
  • Delete event: 7
  • Member event: 6
  • Issue comment event: 22
  • Push event: 45
  • Public event: 1
  • Pull request review comment event: 3
  • Pull request review event: 11
  • Pull request event: 33
  • Fork event: 5

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 78
  • Total Committers: 5
  • Avg Commits per committer: 15.6
  • Development Distribution Score (DDS): 0.5
Past Year
  • Commits: 71
  • Committers: 5
  • Avg Commits per committer: 14.2
  • Development Distribution Score (DDS): 0.535
Top Committers
Name Email Commits
Brian Long b****l@a****g 39
Jordan Sicherman j****n@1****m 15
emilyg e****g@a****g 15
dependabot[bot] 4****] 8
Felipe 8****o 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 2 10xgenomics.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 13
  • Total pull requests: 31
  • Average time to close issues: 9 days
  • Average time to close pull requests: 5 days
  • Total issue authors: 3
  • Total pull request authors: 11
  • Average comments per issue: 1.15
  • Average comments per pull request: 0.39
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 13
  • Pull requests: 30
  • Average time to close issues: 9 days
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 11
  • Average comments per issue: 1.15
  • Average comments per pull request: 0.4
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 8
View more stats
Top Authors
Issue Authors
  • berl (11)
  • kandarpRJ (1)
  • dependabot[bot] (1)
  • jsicherman (1)
Pull Request Authors
  • berl (14)
  • dependabot[bot] (12)
  • egelfan2 (9)
  • jsicherman (4)
  • lukezhang-811 (2)
  • Mmaycon (2)
  • FelipePCarcanholo (2)
  • kandarpRJ (2)
  • ximbao (1)
  • Margery0011 (1)
  • shachafl (1)
Top Labels
Issue Labels
dependencies (1)
Pull Request Labels
dependencies (12) python (9)

Dependencies

.github/workflows/test.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
pyproject.toml pypi
  • anndata *
  • igraph *
  • jupyter *
  • leidenalg *
  • scanpy *
  • scipy *
  • seaborn *
requirements.txt pypi
  • 135 dependencies
setup.py pypi
  • anndata *
  • igraph *
  • jupyter *
  • leidenalg *
  • scanpy *
  • scipy *
  • seaborn *
.github/workflows/check_format.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • psf/black stable composite