Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
-
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary
Keywords
Repository
Peptidoglycan MS1 Analysis Tool
Basic Info
- Host: GitHub
- Owner: Mesnage-Org
- License: lgpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://mesnage-org.github.io/pgfinder
- Size: 70.8 MB
Statistics
- Stars: 5
- Watchers: 3
- Forks: 4
- Open Issues: 19
- Releases: 0
Topics
Metadata Files
README.md
PGFinder
A web-site for processing samples is available at PGFinder. For descriptions of the features of each version please refer to the Releases page or the Changelog. If you wish to use the development version please refer to the Installation and Usage documentation.
For an introduction to Peptidoglycan analysis please refer to the documentation.
Usage
PGFinder is available in two forms: a web-based User Interface (WebUI) at mesnage-org.github.io/pgfinder/ or a command line interface (CLI) Python package.
The command-line programme (find_pg) uses a YAML configuration file as input.
bash
find_pg -c config.yaml
For details of using the CLI version including the configuration file please refer to the Usage section of the Documentation.
Installation
pgfinder
Detailed installation instructions can be found in the Installation section of the Documentation.
PGFinder is available from PyPI so can be installed with pip.
bash
pip install pgfinder
It can also be installed directly from this repository
bash
pip install "git+https://github.com/Mesnage-Org/pgfinder.git#egg=pgfinder&subdirectory=lib"
Or you can clone the repository and install it.
bash
git clone https://github.com/Mesnage-Org/pgfinder.git
cd pgfinder/lib
pip install -e .
WebUI
A WebUI implemented using the Svelte framework is available. Detailed information of development is not currently provided but if you wish to run the WebUI locally you can do so. You will need the npm JavaScript package manager installed and you can then start the WebUI locally using the following and open the URL in your browser.
bash
cd web
npm install
npm install vite # Install the vite framework for building the site
npm run dev
Contributing
Contributions are welcome! Please refer to the detailed
Contributing section of the Documentation which
details how to setup and install all components, and setup/configure the development tools such as pre-commit.
Copying
This software is licensed as specified by the GPL License and LGPL License. Please refer to the
COPYING and
COPYING.LESSER files for further details.
Links
References
- A software tool and strategy for peptidoglycomics, the high-resolution analysis of bacterial peptidoglycans via LC-MS/MS | Communications Chemistry
- PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans | eLife
- PGFinder, an Open-Source Software for Peptidoglycomics: The Structural Analysis of Bacterial Peptidoglycan by LC-MS | SpringerLink
Owner
- Name: Mesnage-Org
- Login: Mesnage-Org
- Kind: organization
- Repositories: 1
- Profile: https://github.com/Mesnage-Org
Citation (CITATION.cff)
cff-version: 1.1.0 message: "If you use this software, please cite it as below." authors: - family-names: Rady given-names: Brooks Joseph orcid: https://orcid.org/0000-0003-4763-4070 - family-names: Patel given-names: Ankur orcid: https://orcid.org/0000-0001-8161-3455 - family-names: Turner given-names: Robert - family-names: Shephard given-names: Neil orcid: https://orcid.org/0000-0001-8301-6857 title: PGFinder version: v1.3.2 date-released: 2025-02-28
GitHub Events
Total
- Create event: 19
- Release event: 1
- Issues event: 12
- Watch event: 1
- Delete event: 48
- Member event: 1
- Issue comment event: 23
- Push event: 52
- Pull request review comment event: 1
- Pull request event: 26
- Pull request review event: 6
- Fork event: 2
Last Year
- Create event: 19
- Release event: 1
- Issues event: 12
- Watch event: 1
- Delete event: 48
- Member event: 1
- Issue comment event: 23
- Push event: 52
- Pull request review comment event: 1
- Pull request event: 26
- Pull request review event: 6
- Fork event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 107
- Total pull requests: 158
- Average time to close issues: 4 months
- Average time to close pull requests: 15 days
- Total issue authors: 4
- Total pull request authors: 8
- Average comments per issue: 3.12
- Average comments per pull request: 2.44
- Merged pull requests: 137
- Bot issues: 0
- Bot pull requests: 41
Past Year
- Issues: 6
- Pull requests: 17
- Average time to close issues: 1 day
- Average time to close pull requests: 10 days
- Issue authors: 3
- Pull request authors: 5
- Average comments per issue: 0.17
- Average comments per pull request: 0.41
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 9
Top Authors
Issue Authors
- ns-rse (38)
- TheLostLambda (28)
- smesnage (25)
- bobturneruk (14)
Pull Request Authors
- ns-rse (55)
- TheLostLambda (42)
- pre-commit-ci[bot] (38)
- bobturneruk (20)
- dependabot[bot] (16)
- Ankur-AVP-Patel (8)
- smesnage (1)
- Navya-Inf (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 164 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 26
- Total maintainers: 1
pypi.org: pgfinder
Peptidoglycan analysis
- Documentation: https://pgfinder.readthedocs.io/en/latest/
- License: GNU Lesser GPLv3
-
Latest release: 1.4.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
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- 313 dependencies
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