ReactomeGSA
R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
Science Score: 36.0%
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
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary
Keywords from Contributors
Repository
R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
Basic Info
- Host: GitHub
- Owner: reactome
- License: other
- Language: R
- Default Branch: master
- Size: 1020 KB
Statistics
- Stars: 26
- Watchers: 2
- Forks: 5
- Open Issues: 23
- Releases: 0
Metadata Files
README.md
ReactomeGSA
The ReactomeGSA package is an R client to the Reactome Analysis System. This new analysis system supports multi-species, multi-omics, comparative pathway analyses.
Getting Help
- For any questions surrounding the use of ReactomeGSA, please simply post it in our Q&A Section
- Should you find a bug in our tool(s) we'd be very grateful if you could report it by posting a new GitHub Issue
- If you encounter any other issues, don't hesitate to contact us at help [at] reactome [dot] org
Documnetation
The complete usage of the package is described in the main vignette.
If you are interested in processing single-cell RNA-seq data using ReactomeGSA, checkout this vignette
Installation
Bioconductor
The ReactomeGSA package is part of Bioconductor since version 3.10. You can find detailed information on the latest stable version on ReactomeGSA's Bioconductor page.
To install the latest version from Bioconductor use
```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("ReactomeGSA") ```
Latest Version
Bioconductor is updated every 6 months. You can still get the latest version of the ReactomeGSA package directly from GitHub:
```r
install devtools if needed
if (!require(devtools)) { install.packages("devtools") }
install the ReactomeGSA package
if (!require(ReactomeGSA)) { install_github("reactome/ReactomeGSA") } ```
Citation
If you used ReactomeGSA in your research, we would be grateful if you could cite the following manuscript:
Griss et al., ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis (2020), MCP 19 (12) P2115-2125, DOI: 10.1074/mcp.TIR120.002155
Owner
- Name: Reactome
- Login: reactome
- Kind: organization
- Email: help@reactome.org
- Location: Canada, US, UK
- Website: https://reactome.org
- Repositories: 99
- Profile: https://github.com/reactome
A curated pathway database
GitHub Events
Total
- Issues event: 2
- Watch event: 9
- Delete event: 1
- Issue comment event: 1
- Push event: 8
- Pull request event: 1
- Fork event: 2
Last Year
- Issues event: 2
- Watch event: 9
- Delete event: 1
- Issue comment event: 1
- Push event: 8
- Pull request event: 1
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Johannes Griss | j****8@y****m | 52 |
| Nitesh Turaga | n****a@g****m | 12 |
| J Wokaty | j****y@s****u | 2 |
| Johannes Griss | j****s | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 69
- Total pull requests: 2
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 months
- Total issue authors: 35
- Total pull request authors: 2
- Average comments per issue: 1.81
- Average comments per pull request: 5.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jgriss (18)
- Ankita-1211 (5)
- FADHLyemen (4)
- bravedu01 (3)
- alexgrent (2)
- vertesy (2)
- jjyotikataria (2)
- camilla0801 (2)
- rpauly (2)
- XjtuZhangKun-lab (2)
- nearvh (1)
- Luq16 (1)
- Byronxy (1)
- cqgong (1)
- querques (1)
Pull Request Authors
- Gionmattia (2)
- alexgrent (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 20,445 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: ReactomeGSA
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
- Homepage: https://github.com/reactome/ReactomeGSA
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ReactomeGSA/inst/doc/ReactomeGSA.pdf
- License: MIT + file LICENSE
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Latest release: 1.22.0
published about 1 year ago