software-landscape-analysis
Enabling software landscape analyses to better understand existing efforts or solutions.
Science Score: 44.0%
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
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Repository
Enabling software landscape analyses to better understand existing efforts or solutions.
Basic Info
- Host: GitHub
- Owner: WayScience
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://wayscience.github.io/software-landscape-analysis/
- Size: 16.6 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Landscape Analysis
A "landscape analysis" is an informational survey of existing software and other tooling that solve similar problems or use similar technologies. This repository performs landscape analyses for specific projects.
Installation
Please use Python poetry to run and install related content.
```bash
after installing poetry, create the environment
poetry install ```
Development
Jupyter Lab
Please follow installation steps above and then use a relevant Jupyter environment to open and explore the notebooks under the notebooks directory.
```bash
after creating poetry environment, run jupyter
poetry run jupyter lab ```
Poe the Poet
We use Poe the Poet to define and run tasks defined within pyproject.toml under the section [tool.poe.tasks*].
This allows for the definition and use of a task workflow when implementing multiple procedures in sequence.
For example, use the following to run the cytomining_ecosystem task:
```bash
run cytomining_ecosystem using poethepoet
poetry run poe cytominingecosystemfall_2023 ```
Reports and GitHub Pages
We use a GitHub Pages URL at https://wayscience.github.io/software-landscape-analysis/ to help share data analysis reports with others.
For example, Plotly HTML exports can be added to the relevant location and shared via a link.
Contents under the /docs directory is used as a reference for GitHub Actions-based deployments which occur automatically on merge with the main branch.
Owner
- Name: The Way Lab
- Login: WayScience
- Kind: organization
- Location: United States of America
- Website: https://waysciencelab.com
- Repositories: 17
- Profile: https://github.com/WayScience
The Way Lab at CU Anschutz
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
---
cff-version: 1.2.0
title: software-landscape-analysis
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: David
family-names: Bunten
orcid: 'https://orcid.org/0000-0001-6041-3665'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
repository-code: 'https://github.com/WayScience/software-landscape-analysis'
url: 'https://github.com/WayScience/software-landscape-analysis'
abstract: >-
Enabling software landscape analyses to better understand existing efforts or solutions.
keywords:
- way-lab
- python
- jupyter
- software-landscape-analysis
license: BSD-3-Clause
references:
- authors:
- family: Zappia
given: Luke
- family: Phipson
given: Belinda
- family: Oshlack
given: Alicia
title: Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
version: ""
doi: "10.1371/journal.pcbi.1006245"
url: "https://doi.org/10.1371/journal.pcbi.1006245"
year: 2018
journal: PLoS Computational Biology
volume: 14
number: 6
pages: e1006245
notes: >-
scRNA-tools database table extract is referenced as part of analysis found under notebooks/cytomining-ecosystem.
An export of the data is saved as: notebooks/cytomining-ecosystem/scRNA-Tools-tableExport-2023-10-12.csv
- title: scholarly
abstract: Retrieve author and publication information from Google Scholar in a friendly, Pythonic way without having to worry about CAPTCHAs!
type: software
license: The Unlicense, Open Access
version: 1.5.0
url: https://zenodo.org/record/5764801
keywords:
- citations publication-data scholarly-communications citation-network citation-index scholarly-articles citation-analysis scholar googlescholar
authors:
- family-names: Cholewiak
given-names: Steven
- family-names: Ipeirotis
given-names: Panos
- family-names: Silva
given-names: Victor
- family-names: Kannawadi
given-names: Arun
date-released: 2023-01-16
identifiers:
- type: doi
value: 10.5281/ZENODO.5764801
- title: BiorxivRetriever
authors:
- family-names: Schuster
given-names: Tal
type: software
license: MIT
url: https://github.com/TalSchuster/BiorxivRetriever/
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Dependencies
- JamesIves/github-pages-deploy-action v4 composite
- actions/checkout v4 composite
- actions/checkout v4 composite
- actions/setup-python v4 composite
- pre-commit/action v3.0.0 composite
- 280 dependencies
- aiohttp ^3.8.6
- awkward ^2.4.10
- biorxiv-retriever ^0.20.1
- condastats ^0.2.1
- duckdb ^0.9.0
- fsspec ^2023.10.0
- github-dependents-info ^1.2.0
- google-cloud-bigquery ^3.13.0
- htmlmin ^0.1.12
- intake ^0.7.0
- intake-parquet ^0.3.0
- ipywidgets ^8.1.1
- itables ^1.6.2
- matplotlib >=3.2,<=3.7.3
- nest-asyncio ^1.5.8
- numpy >=1.16.0,<1.26
- pandas >=2.0.0,<3.0.0
- plotly ^5.17.0
- poethepoet ^0.24.1
- poetry ^1.6.1
- pyarrow >=14.0.0
- pygithub ^2.1.1
- pypinfo ^21.0.0
- pyppeteer ^1.0.2
- python >=3.9,<3.12
- python-box ^7.1.1
- pytz ^2023.3.post1
- requests ^2.31.0
- s3fs ^2023.10.0
- scholarly ^1.7.11
- thefuzz ^0.20.0
- ydata-profiling ^4.6.0