nvr
NVR is a python implementation of gene feature selection used in Welch et al.,2016
Science Score: 20.0%
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
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Repository
NVR is a python implementation of gene feature selection used in Welch et al.,2016
Basic Info
- Host: GitHub
- Owner: KenLauLab
- License: gpl-2.0
- Language: Jupyter Notebook
- Default Branch: master
- Size: 29.4 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 5
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
NVR (neighborhood variance ratio)
Python implementation of NVR (neighborhood variance ratio) gene selection to select genes with local and monotonic variation (Welch et al., 2016). The selected genes possess specific expression patterns over the entire data space amenable to trajectory analysis. Support for python 2 is now deprecated with version 0.1.0 scanpy integration, as scanpy requires python 3.
Installation for Mac or Linux
NVR requires igraph and scanpy for operation, so please see our instructions for the installation of these packages.
There are two ways to install NVR with Mac/Linux operating systems.
1.
python
git clone git://github.com/KenLauLab/NVR
cd NVR
pip install .
2.
python
pip install nvr #this needs to be updated so avoid doing this for now
Installation for Windows (in Anaconda3 environment)
In your anaconda terminal, navigate to a directory where you want to install NVR (e.g. d:\src)
cd d:\src
git clone git://github.com/KenLauLab/NVR
cd NVR
pip install .
Tutorial
Please see the NVR running .ipynb tutorial as well as its associated dataset
Owner
- Login: KenLauLab
- Kind: user
- Location: Nashville, TN
- Website: https://www.mc.vanderbilt.edu/vumcdept/cellbio/laulab/people.html
- Repositories: 5
- Profile: https://github.com/KenLauLab
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| bobchen1701 | 3****1 | 9 |
| KenLauLab | c****g@v****u | 8 |
| Bob | b****b@m****u | 4 |
| Bob Chen | b****n@v****u | 4 |
| JP Cartailler | c****e | 2 |
| Bob | b****b@M****l | 1 |
| KenLauLab | 3****b | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 4
- Total pull requests: 2
- Average time to close issues: 9 months
- Average time to close pull requests: 9 minutes
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- codyheiser (3)
- bobchen1701 (1)
Pull Request Authors
- c5creative (1)
- KenLauLab (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 72 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 4
- Total maintainers: 1
pypi.org: nvr
python implementation of gene feature selection used in Welch et al.,2016
- Homepage: https://github.com/KenLauLab/NVR
- Documentation: https://nvr.readthedocs.io/
- License: gpl-2.0
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Latest release: 0.0.6
published over 8 years ago
Rankings
Maintainers (1)
Dependencies
- networkx *
- numpy >=1.11.0
- pandas >=0.17.1
- scanpy *
- scipy >=0.17.0