Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Keywords
Repository
A Python API for managing genotype-phenotype map data
Basic Info
Statistics
- Stars: 12
- Watchers: 10
- Forks: 8
- Open Issues: 4
- Releases: 9
Topics
Metadata Files
README.md
GPMap
A Python API for managing genotype-phenotype map data
GPMap defines a flexible object for managing genotype-phenotype (GP) map data. At it's core, it stores all data in Pandas DataFrames and thus, interacts seamlessly with the PyData ecosystem.
To visualize genotype-phenotype objects created by GPMap, checkout GPGraph.
Basic example
Import the package's base object.
python
from gpmap import GenotypePhenotypeMap
Pass your data to the object. ```python
Data
wildtype = "AAA" genotypes = ["AAA", "AAT", "ATA", "TAA", "ATT", "TAT", "TTA", "TTT"] phenotypes = [0.1, 0.2, 0.2, 0.6, 0.4, 0.6, 1.0, 1.1] stdeviations = [0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05]
Initialize the object
gpm = GenotypePhenotypeMap(wildtype, genotypes, phenotypes, stdeviations=stdeviations)
Check out the data.
gpm.data
```
Or load a dataset from disk.
python
gpm = GenotypePhenotypeMap.read_json("data.json")
Installation
Users
This simplest way to install this package is using pip:
pip install gpmap
Developers
The recommended way to install this package for development is using pipenv.
- Clone this repository:
git clone https://github.com/harmslab/gpmap - Install the package using pipenv.
cd gpmap pipenv install --dev -e . - Run tests using pytest
pytest
Dependencies
The following modules are required. Also, the examples/tutorials are written in Jupyter notebooks and require IPython to be installed.
Owner
- Name: Harms Lab @ University of Oregon
- Login: harmslab
- Kind: organization
- Location: Eugene, OR
- Website: http://harmslab.uoregon.edu
- Repositories: 57
- Profile: https://github.com/harmslab
Software projects created by members of the the Harms lab at the University of Oregon
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zachary Sailer | z****r@g****m | 259 |
| Luis Perez | l****o@u****u | 14 |
| Michael J. Harms | h****m@g****m | 11 |
| Luis Perez Morales | 6****o | 8 |
| lgoldbach | l****h@s****l | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 32
- Average time to close issues: over 1 year
- Average time to close pull requests: 27 days
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 3.8
- Average comments per pull request: 0.44
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 8
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
- Zsailer (2)
- 326reborn (1)
- joneill-code (1)
- jamaltas (1)
Pull Request Authors
- Zsailer (16)
- dependabot[bot] (8)
- harmsm (6)
- lgoldbach (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 222 last-month
- Total dependent packages: 0
- Total dependent repositories: 7
- Total versions: 15
- Total maintainers: 3
pypi.org: gpmap
A Python API for managing genotype-phenotype map data
- Homepage: https://github.com/harmslab/gpmap
- Documentation: https://gpmap.readthedocs.io/
- License: MIT
-
Latest release: 0.7.0
published over 5 years ago
Rankings
Dependencies
- gpmap * develop
- gpmap *
- matplotlib *
- numpy *
- pandas *
- pytest *
- scipy *
- gpmap * develop
- numpy ==1.19.1 develop
- pandas ==1.1.0 develop
- python-dateutil ==2.8.1 develop
- pytz ==2020.1 develop
- scipy ==1.5.2 develop
- six ==1.15.0 develop
- atomicwrites ==1.4.0
- attrs ==19.3.0
- certifi ==2020.6.20
- colorama ==0.4.3
- cycler ==0.10.0
- gpmap *
- importlib-metadata ==1.7.0
- iniconfig ==1.0.1
- kiwisolver ==1.2.0
- matplotlib ==3.3.1
- more-itertools ==8.4.0
- numpy ==1.19.1
- packaging ==20.4
- pandas ==1.1.0
- pillow ==7.2.0
- pluggy ==0.13.1
- py ==1.9.0
- pyparsing ==2.4.7
- pytest ==6.0.1
- python-dateutil ==2.8.1
- pytz ==2020.1
- scipy ==1.5.2
- six ==1.15.0
- toml ==0.10.1
- zipp ==3.1.0
- ipython *
- atomicwrites ==1.2.1
- attrs ==18.2.0
- matplotlib *
- more-itertools ==4.3.0
- numpy >=1.15.2
- pandas >=0.24.2
- py ==1.6.0
- pytest >=3.8.1
- scipy >=1.1.0
- actions/checkout v2 composite
- actions/setup-python v2 composite