https://github.com/alleninstitute/abc_atlas_access
Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
4 of 7 committers (57.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary
Repository
Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- License: other
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://alleninstitute.github.io/abc_atlas_access/
- Size: 1.29 GB
Statistics
- Stars: 81
- Watchers: 12
- Forks: 28
- Open Issues: 26
- Releases: 11
Metadata Files
README.md
Allen Brain Cell Atlas - Data Access
The Allen Brain Cell Atlas (ABC Atlas) aims to empower researchers worldwide to explore and analyze multiple whole-brain datasets simultaneously. As the Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas, this groundbreaking platform will keep growing, opening up endless possibilities for groundbreaking discoveries and breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can gain new insights into the brains complex workings, advancing our understanding of this amazing organ in ways we never thought possible.
ABC Atlas Data Access JupyterBook Website
https://AllenInstitute.github.io/abcatlasaccess
How to contribute
JupyterBook Contribution Guide
Note: for scientific questions regarding the data this repository is accessing, please use the Allen Institute's community forum. If you are having an issue with the code or notebooks not running properly please open an issue on this Github repository. However, please see below.
Level of support
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
Installation
To install base package with the cache object in your python environment, use pip with the following command:
console
pip install git+https://github.com/alleninstitute/abc_atlas_access.git
To install the package with all optional dependencies, specifically those needed to re-run the notebooks, you can use the following command:
console
pip install "abc_atlas_access[notebooks] @ git+https://github.com/alleninstitute/abc_atlas_access.git"
We assume that you already have Jupyter installed if you are re-running the notebooks. Running the getting_started notebook will also help you install the package.
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Create event: 22
- Release event: 5
- Issues event: 20
- Watch event: 31
- Issue comment event: 18
- Push event: 162
- Pull request review comment event: 2
- Pull request review event: 12
- Pull request event: 26
- Fork event: 5
Last Year
- Create event: 22
- Release event: 5
- Issues event: 20
- Watch event: 31
- Issue comment event: 18
- Push event: 162
- Pull request review comment event: 2
- Pull request review event: 12
- Pull request event: 26
- Fork event: 5
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lydia Ng | 8****g | 149 |
| Christopher Morrison | c****n@a****g | 26 |
| Puja Trivedi | p****i@P****l | 21 |
| danielsf | s****l@a****g | 9 |
| Xingjie Pan | x****n@g****m | 3 |
| Jeremy Miller | j****m@a****g | 1 |
| Ashwin Bhandiwad | a****d@a****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 29
- Total pull requests: 65
- Average time to close issues: about 2 months
- Average time to close pull requests: 13 days
- Total issue authors: 17
- Total pull request authors: 10
- Average comments per issue: 0.62
- Average comments per pull request: 0.42
- Merged pull requests: 47
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 13
- Pull requests: 25
- Average time to close issues: 21 days
- Average time to close pull requests: 17 days
- Issue authors: 8
- Pull request authors: 2
- Average comments per issue: 0.46
- Average comments per pull request: 0.16
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- morriscb (8)
- stefanonard85 (2)
- tmchartrand (2)
- ShaowenJCornell (1)
- lydiang (1)
- jackwalleninstituteorg (1)
- Super-LzzZ (1)
- Counts-Xin (1)
- KatMedMed (1)
- danielsf (1)
- puja-trivedi (1)
- chrism-reid (1)
- seasonzhao (1)
- rwollman (1)
- ayeTown (1)
Pull Request Authors
- morriscb (60)
- lydiang (16)
- puja-trivedi (2)
- danielsf (2)
- djarecka (1)
- xingjiepan (1)
- zrlewis (1)
- jeremymiller (1)
- neurovium (1)
- tmchartrand (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- peaceiris/actions-gh-pages v3.6.1 composite
- SimpleITK *
- anndata *
- ghp-import *
- jupyter-book *
- matplotlib *
- numpy *
- pandas *
- requests *
- scipy *