https://github.com/alleninstitute/cell_type_mapper
Repository for storing prototype functionality implementations for the BKP
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
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Repository
Repository for storing prototype functionality implementations for the BKP
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- License: other
- Language: Python
- Default Branch: main
- Size: 38.7 MB
Statistics
- Stars: 33
- Watchers: 6
- Forks: 7
- Open Issues: 8
- Releases: 0
Metadata Files
README.md
Cell Type Mapper
Overview
This code provides a python package for mapping single sell RNA sequencing data onto a cell type taxonomy such as that provided by the Allen Institute for Brain Science.
Installation
To install this library, clone the repository, then (ideally from a clean python environment)
- Run
pip install -e .from the root directory of this repository to install this package itself.
This package has been tested extensively with python 3.9. We have no reason to believe that it will not also run with python 3.8 and 3.10.
Common use cases
In addition to the documentation referenced below, we provide several Jupyter notebooks detailing common use cases for this code.
Submitting data to online MapMyCells tool
The code in this repository provides the backend for the Allen Institute's online MapMyCells tool. This notebook walks the user through the process of downloading actual data, formatting it to be submitted to MapMyCells, and then downloading and interpreting the results. You may also want to consult this page for detailed documentation of the output produced by the mapping code.
Mapping to Allen Institute taxonomies on your own machine
If you want to run the code on your own machine, but still want to map to the taxonomies supported by the on-line MapMyCells tool, consult this page and Section 8 of this Jupyter notebook.
Mapping to a user-defined taxonomy
This Jupyter notebook walks the user through the process of creating a new taxonomy from cartoon data (generated by the notebook) and mapping unlabeled data to that taxonomy.
Creating and mapping to a taxonomy defined from a subset of the Allen Institute's data
This Jupyter notebook walks the user through the process of downloading a subset of the Allen Institute's Whole Mouse Brain data using the abcatlasaccess tool, creating a taxonomy based solely on that subset of the data, and mapping data to that new taxonomy.
Detailed documentation
The recommended workflow for running this code is here.
Documentation of the output produced by this code can be found here.
Level of support
We are providing this tool to the community and any and all who want to use it. Issues and pull requests are welcome, however, this code is also intended as part of the backend for the Allen Institute Brain Knowledge Platform. As such, issues and pull requests may be declined if they interfere with the functionality required to support that service.
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
- Issues event: 11
- Watch event: 14
- Delete event: 2
- Issue comment event: 47
- Push event: 237
- Pull request event: 6
- Fork event: 3
- Create event: 35
Last Year
- Issues event: 11
- Watch event: 14
- Delete event: 2
- Issue comment event: 47
- Push event: 237
- Pull request event: 6
- Fork event: 3
- Create event: 35
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| danielsf | s****l@a****g | 1,883 |
| Carlos Caceres | c****a@a****m | 14 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 20
- Total pull requests: 19
- Average time to close issues: 3 months
- Average time to close pull requests: 5 days
- Total issue authors: 20
- Total pull request authors: 3
- Average comments per issue: 5.25
- Average comments per pull request: 0.42
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 11
- Pull requests: 7
- Average time to close issues: about 1 month
- Average time to close pull requests: 6 days
- Issue authors: 11
- Pull request authors: 1
- Average comments per issue: 6.09
- Average comments per pull request: 0.43
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- danielsf (2)
- Winterwind (1)
- mtvector (1)
- inkarkapen (1)
- berl (1)
- mitsiask (1)
- kulansam (1)
- scseeman (1)
- siennasage18 (1)
- beyondpie (1)
- zyll123 (1)
- Xieeeee (1)
- an-altosian (1)
- KatMedMed (1)
- mbatiuk (1)
Pull Request Authors
- danielsf (13)
- cacerca (7)
- inkarkapen (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- anndata *
- argschema *
- marshmallow ==3.12.2
- matplotlib *
- numpy *
- pytest *
- scipy *
- zarr *