connectivity-search-analyses
hetnet connectivity search research notebooks (previously hetmech)
Science Score: 44.0%
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Low similarity (13.3%) to scientific vocabulary
Keywords
Repository
hetnet connectivity search research notebooks (previously hetmech)
Basic Info
Statistics
- Stars: 9
- Watchers: 7
- Forks: 5
- Open Issues: 6
- Releases: 0
Topics
Metadata Files
README.md
Hetnet connectivity search prototyping and data repository
Connectivity Search (formerly called Hetmech for hetnet mechanisms) is a project to extract mechanistic connections between nodes in hetnets. The project aims to identify the relevant network connections between query nodes. The method is designed to operate on hetnets (networks with multiple node or relationship types).
Note: the hetmech python package has been renamed to hetmatpy and relocated to hetio/hetmatpy.
This repository is now used as a historical archive,
as well as a dataset storage, method prototyping, and exploratory data analysis repository.
Many findings from this repository are described in the Connectivity Search Manuscript.
The manuscript source code is available in greenelab/connectivity-search-manuscript.
Environment
This repository uses conda to manage its environment as specified in environment.yml.
Install the environment with:
```sh
install new hetmech environment
conda env create --file=environment.yml
update existing hetmech environment
conda env update --file=environment.yml ```
Then use conda activate hetmech and conda deactivate to activate or deactivate the environment.
Note that the environment is tested with the conda channel_priority strict configuration.
Locally, you can run the following commands to configure conda (as per https://conda-forge.org docs),
but note that it affects your conda config beyond this environment:
shell
conda config --add channels conda-forge
conda config --set channel_priority strict
Another option is to install conda with miniforge.
Acknowledgments
This work was supported through a research collaboration with Pfizer Worldwide Research and Development. This work was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants GBMF4552 to Casey Greene and GBMF4560 to Blair Sullivan.
Owner
- Name: Greene Laboratory
- Login: greenelab
- Kind: organization
- Email: casey@greenelab.com
- Location: Aurora, CO
- Website: https://www.greenelab.com
- Twitter: greenescientist
- Repositories: 162
- Profile: https://github.com/greenelab
Greene Laboratory at the University of Colorado Anschutz
Citation (CITATION.cff)
cff-version: 1.2.0
title: >-
greenelab/connectivity-search-analyses repository:
Hetnet connectivity search research notebooks
message: >-
This citation is for the code and data repository.
To cite Hetnet connectivity search more generally,
see the manuscript at <https://greenelab.github.io/connectivity-search-manuscript/>.
type: software
authors:
- given-names: Daniel
family-names: Himmelstein
orcid: 'https://orcid.org/0000-0002-3012-7446'
- given-names: Michael
family-names: Zietz
orcid: 'https://orcid.org/0000-0003-0539-630X'
- given-names: Kyle
family-names: Kloster
orcid: 'https://orcid.org/0000-0001-5678-7197'
- given-names: Benjamin
family-names: Heil
orcid: 'https://orcid.org/0000-0002-2811-1031'
- given-names: Yun
family-names: Hao
orcid: 'https://orcid.org/0000-0002-1684-0085'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
- given-names: Michael
family-names: Nagle
orcid: 'https://orcid.org/0000-0002-4677-7582'
- given-names: Blair
family-names: Sullivan
orcid: 'https://orcid.org/0000-0001-7720-6208'
- given-names: Casey
family-names: Greene
orcid: 'https://orcid.org/0000-0001-8713-9213'
identifiers:
- type: swh
value: 'swh:1:rev:15f1925c0481d8e6bab8b0931f48f2fad388c68c'
description: Software Heritage Revision Snapshot
- type: swh
value: 'swh:1:dir:9444ce4d64e6e45c6bf896ecb926ea6676d8e821'
description: Software Heritage Directory Snapshot
repository-code: 'https://github.com/greenelab/connectivity-search-analyses'
abstract: >-
The initial project repository for Hetnet Connectivity Search that contains research notebooks, dataset generation code, and exploratory data analyses.
The hetmatpy package was first developed as part of this repository until its [relocation](https://github.com/hetio/hetmatpy/issues/1) in November 2018.
This repository was formerly named hetmech.
keywords:
- matrix
- numpy
- scipy
- hetionet
- networks
- mechanism
- hetmech
- theory-in-practice
- hetmat
- networks
- hetio
- hetmech
- hetnets
- hetnet-connectivity-search
license: BSD-3-Clause
GitHub Events
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Last Year
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 54
- Total pull requests: 110
- Average time to close issues: 6 months
- Average time to close pull requests: 8 days
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 5.0
- Average comments per pull request: 2.54
- Merged pull requests: 89
- 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
- dhimmel (18)
- kkloste (7)
- zietzm (5)
- gwaybio (2)
- NegarJanani (1)
- mutandon (1)
Pull Request Authors
- dhimmel (32)
- zietzm (26)
- kkloste (5)
- naglem (3)
- gwaybio (1)
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Dependencies
- flake8 3.8.4.*
- ipykernel 5.4.2.*
- ipywidgets 7.6.2.*
- nb_conda_kernels 2.3.1.*
- neo4j-python-driver 4.2.1.*
- notebook 6.1.6.*
- numpy 1.19.4.*
- pandas 1.2.0.*
- pip
- plotly 4.14.1.*
- plotnine 0.7.1.*
- psycopg2 2.8.6.*
- py2neo 4.2.0.*
- pytest 6.2.1.*
- python 3.8.6.*
- requests 2.25.1.*
- scikit-learn 0.24.0.*
- scikit-misc 0.1.3.*
- scipy 1.6.0.*
- tqdm 4.55.1.*
- umap-learn 0.4.6.*
- xarray 0.16.2.*
- xlrd 1.2.0.*